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PubMedDate not supplied

Characterization of RTG-2 fish cell line by random amplified polymorphic DNA.

The increasing presence of genotoxic chemicals in the aquatic environment has led to the development of both in vivo and in vitro assays for target species. The fish population represents an important level of aquatic ecosystems that can be threatened by increased environmental pollution. The authors have studied the DNA pattern of the RTG-2 fish cell line, a fibroblast-like cell line, derived from rainbow trout (Oncorhynchus mikyss), to use this cell line as an in vitro system to study genotoxicity by means of random amplified polymorphic DNA primers (RAPDs). A constant pattern in the DNA band is essential when an organism or cell line is used to detect DNA alterations produced by genotoxic environmental chemicals. DNA fingerprints with RAPDs were obtained for RTG-2 by testing 26 single and 70 pairwise combinations of primers. Different methods of DNA extraction (chelating resin, salting out, and phenolization), the influence of spectrometric measures at 320 nm in the 260/280 quotient to quantify DNA extracts, genomic DNA and primer concentrations, annealing temperatures, and cell line passage were studied in the cell line characterization. RAPD products were identified by agarose gel electrophoresis. The good results obtained should allow the use of this system as a possible tool for detection of the genotoxicity of aquatic pollutants.

Animals↗
PubMed1998

RAPD analysis of Candida albicans strains recovered from different immunocompromised patients (ICP) reveals an apparently non-random infectivity of the strains.

The opportunistic imperfect fungus Candida albicans causing life-threatening infections in immunocompromised patients (ICP), especially in HIV-positive cases, is recognized to be one of the most important nosocomial pathogens in the recent decades. The extent of strain-to-strain variation within a species and its relationship to the ability of the organism to colonize or invade a specific group of patients or even a body site is, however, not well known. We have analysed 19 strains of C. albicans recovered from ICP at different locales and times, employing the RAPD technique. No two strains generated identical RAPD profiles with any of the 21 primers tested. Further, the UPGMA clustering of the strains seemingly reflected a certain relationship or nonrandomness in the infection of the patients with the strain of C. albicans vis-a-vis the immunocompromised status due to underlying disease such as diabetes, cancer, asthma and meningitis. These results may have a profound impact on the management of candidiasis, especially in the ICP.

Candida albicans↗
PubMed2004

Candida parapsilosis detected in TPN using the BacT/Alert system and characterized by randomly amplified polymorphic DNA.

Candida parapsilosis was detected in environmental swabs and batches of total parenteral nutrition (TPN) products after routine monitoring. The isolates were analysed using randomly amplified polymorphic DNA (RAPD) to determine clonality and establish the most likely source of contamination. Of 20 isolates analysed, 18 were indistinguishable clonally and were found to be associated with particular work stations. The application of regular testing using a system such as the BacT/Alert, and molecular studies for epidemiological analysis, is of benefit to producers of medical products such as TPN to ensure patient safety.

Candida↗
PubMed2001

Incorporating the ABI GeneScan analysis to a RACE-based technique for mapping multiple transcription initiation sites.

Determination of transcription initiation sites has commonly been performed by primer extension and RNase protection assay using radioactively labeled oligonucleotides. Recently, a protocol based on modified 5' rapid amplification of cDNA ends (RACE) with the use of fluorescently labeled primer was developed. Here, we describe the use of RACE-based technique in conjunction with the GeneScan analysis for the determination of transcription initiation sites of genes of interest. The RACE technique is based on the ligation of an adapter to both ends of the cDNAs. The gene of interest was first amplified by PCR using a gene-specific and a 5' adapter primer. Subsequently, nested PCR was performed using an internal gene-specific primer paired with a fluorescently end-labeled adapter primer. The size of the fluorescently labeled PCR products was directly determined by the ABI PRISM 377 GeneScan Analyzer. This novel approach provides an accurate, sensitive, and convenient method for mapping transcription initiation sites, especially for genes with multiple transcription initiation sites, for genes expressed at low levels, and for splice variants that display alternative splicing farther than a few hundred nucleotides downstream from the transcription initiation site. This article describes the application of this new method in the mapping of transcription initiation sites of two splice variants of rat frizzled related protein transcripts.

Alternative Splicing↗
PubMed2002

Molecular detection and characterization of Neisseria meningitidis.

Immediate management of meningococcal infections is a medical emergency that requires rapid identification and typing of bacterial strains. Isolation of Neisseria meningitidis is hindered by early antibiotic treatment. Molecular (nonculture) methods of diagnosis and characterization of N. meningitidis permit to overcome this failure. This bacterium is highly variable due to frequent horizontal DNA exchange between strains. Molecular approaches of typing allow a reliable tracking of meningococcal strains and a powerful epidemiological analysis.

DNA Fingerprinting↗
PubMed2006

Monitoring the cell number of Lactococcus lactis subsp. cremoris FC in human feces by real-time PCR with strain-specific primers designed using the RAPD technique.

Strain-specific PCR primers for Lactococcus lactis subsp. cremoris FC were developed using the randomly amplified polymorphic DNA (RAPD) technique. RAPD was used to generate strain-specific markers. A 1164-bp RAPD marker found to be strain-specific was sequenced, and a primer pair specific for L. lactis subsp. cremoris FC was designed. The specificity of this primer pair was tested with 23 L. lactis subsp. cremoris strains and 20 intestinal bacterial species, and was found to be strain-specific. Subsequently, this primer pair was subjected to the quantification of L. lactis subsp. cremoris FC in the feces of subjects fed fermented milk containing this strain. After administration, L. lactis subsp. cremoris FC was detected in the feces of all 7 subjects, with the maximum number being between 10(5) and 10(9) cells g(-1) of feces. Furthermore, this strain was detected in only one feces sample 2 weeks after administration was stopped. These results suggest that L. lactis subsp. cremoris FC can survive passage through the gastrointestinal tract.

Adult↗
PubMed2005

Identification of yeasts associated with milk products using traditional and molecular techniques.

An integrated approach including phenotypic (morphological, biochemical and physiological characterization) and genotypic (RAPD-PCR, sequencing of D1/D2 domain of 26S rRNA encoding gene) methods was used for the identification of yeasts isolated from different milk products. There were 513 isolates in all, 460 ascomycetous and 53 basidiomycetous yeasts. The yeast isolates were characterized on the basis of their biochemical and physiological properties, and the D1/D2 domain of 26S rDNA was sequenced in selected strains. Relying on the obtained results from both the data-sets, corresponding type strains were selected and compared with the respective yeast isolates from milk products by RAPD fingerprinting. The strains showing a degree of similarity >80% were considered conspecific. By means of the applied techniques it was possible to identify 92% yeast isolates at species level. Debaryomyces hansenii, Geotrichum candidum, Kluyveromyces marxianus, Yarrowia lipolytica and Candida zeylanoides are the most frequently isolated species. The majority of the yeasts were isolated from fresh and sour curd cheese. A comparison of the results obtained by phenotypic and genotypic investigation revealed that the identification based on classical methods was supported by genotypic characterization in only 54% of examined isolates. The results described in this work show that the applied molecular identification is a reliable approach to the identification of yeasts associated with milk products in contrast to the conventional biochemical and physiological tests. The identification of new yeast species requires additional genetic markers such as sequencing of different genes or DNA:DNA hybridization.

Colony Count, Microbial↗
PubMed2003

Characterization of yeast isolates originating from Hungarian dairy products using traditional and molecular identification techniques.

Yeast isolates collected from various Hungarian dairy products were identified using simplified identification system (SIM) and restriction fragment analysis of PCR-amplified 18S rDNA with the neighbouring ITS1 region (ITS-PCR; ribotyping). The isolates were grouped into 26 species; Geotrichum candidum, Debaryomyces hansenii, Yarrowia lipolytica, Kluyveromyces lactis and Candida catenulata were found as the predominant species. SIM and ITS-PCR proved to be useful and convenient taxonomic tools for rapid identification at species level. Two most frequent species, G. candidum and D. hansenii, were further characterized by randomly amplified polymorphic DNA (RAPD-PCR) analysis. RAPD-PCR using M13 primer resulted in discrimination between most strains of the same species and allowed a certain degree of intraspecific typing.

Dairy Products↗
PubMed2003

Genotyping of clinical Rhodotorula mucilaginosa isolates by pulsed field gel electrophoresis.

Identification and typing of fungal isolates is a prerequisite for control and prevention of nosocomial infections. As the discriminatory power of phenotypic methods is not sufficient for epidemiological purposes, genotyping methods such as DNA fingerprinting, random amplification of polymorphic DNA (RAPD) analysis, or pulsed field gel electrophoresis (PFGE) are preferred. To our knowledge, this study is the first application of PFGE for typing Rhodotorula mucilaginosa strains. The PFGE patterns of six clinical isolates produced two different karyotypes, which were confirmed by RAPD analysis. Five strains isolated from bloodstream infections from three different institutions showed the same karyotype and RAPD patterns, while the urological specimen differed slightly.

DNA Fingerprinting↗
PubMed1995

DNA fingerprinting by random amplified polymorphic DNA and restriction fragment length polymorphism is useful for yeast typing.

Random amplified polymorphic DNA (RAPD) analysis was applied to genomic DNA from nineteen yeast strains belonging to the genera Saccharomyces and Zygosaccharomyces. Results obtained with five primers indicated that this technique is a powerful tool for yeast differentiation and identification. The data were consistent with those derived from restriction fragment length polymorphism (RFLP) using two S. cerevisiae DNA probes. We conclude that RAPD fingerprinting, combined with the analysis of RFLP, can provide unambiguous type assignment in yeasts.

DNA, Bacterial↗
PubMed1999

Correlation between polymerase chain reaction analysis of the histidine biosynthesis operon, randomly amplified polymorphic DNA analysis and phenotypic characterization of dairy Lactococcus isolates.

A collection of 32 lactococcal strains isolated from raw milk in the Camembert RDO (registered designation of origin) area were phenotypically and genotypically characterized. As expected for environmental isolates, all strains had a Lactococcus lactis subsp. lactis phenotype. The strains were then genotypically identified by the randomly amplified polymorphic DNA (RAPD) technique, using reference strains of lactococci. Two major clusters were identified containing the two subspecies lactis and cremoris. The subspecies lactis cluster could be divided into five subgroups whereas there was a high coefficient of similarity between all strains in the subspecies cremoris cluster. This RAPD classification was then compared with that of a traditional PCR assay using L. lactis species-specific primers corresponding to part of the histidine biosynthesis operon. The two subspecies were differentiated by the size of the fragment amplified (about 200 bp longer for subspecies cremoris). Unlike preliminary phenotypic assignments, the results of PCR experiments corroborated the genotypic identification of the lactococcal strains by RAPD allowing the technique to be reconsidered on the basis of its taxonomic efficiency.

Animals↗
PubMed1999

Identification of CARE-2-negative Candida albicans isolates as Candida dubliniensis.

Among 302 clinical yeast isolates originally identified as Candida albicans, we found 16 isolates that did not hybridize with the C. albicans-specific repetitive DNA element CARE-2. These 16 isolates produced abundant chlamydospores, did not grow at 43 degrees C, and exhibited a distinct randomly amplified polymorphic DNA profile. Sequence analysis of part of the 28S rDNA demonstrated that the CARE-2-negative isolates are not an atypical subgroup of C. albicans but belong to the recently described new species C. dubliniensis.

Candida↗
PubMed2002

Differentiation of Aspergillus ustus strains by random amplification of polymorphic DNA.

The sodium dodecyl sulfate-polyacrylamide gel electrophoresis patterns of water-soluble proteins and the randomly amplified polymorphic DNA (RAPD) patterns of whole-cell lysates from 21 Aspergillus ustus isolates, including 11 reference strains and 10 patient and environmental strains from one hospital, were investigated. All isolates showed identical protein patterns. The RAPD assay discriminated between all reference strains. Comparison of hospital isolates showed identical RAPD patterns in some of the patient and environmental isolates. The data indicate that the RAPD technique is useful for fingerprinting A. ustus.

Aspergillosis↗
PubMed2000

Molecular typing of Histoplasma capsulatum isolated from infected bats, captured in Mexico.

The present paper represents data on the genetic polymorphism of 13 Histoplasma capsulatum isolates recovered from infected bats randomly captured in the Mexican states of Morelos, Puebla, and Oaxaca. The polymorphic DNA patterns were analyzed by two-primer RAPD-PCR (random amplified polymorphic DNA-polymerase chain reaction) method. To amplify the fungal genome by PCR, the following primer arrangements were used: 5'-AACGCGCAAC-3' and 5'-AAGAGCCCGT-3'; 5'-AACGCGCAAC-3' and 5'-GTTTCCGCCC-3'; or 5'-AACGCGCAAC-3' and 5'-GCGATCCCCA-3'. A common polymorphic DNA pattern of H. capsulatum was revealed in different assays. This pattern is shared by 7 H. capsulatum isolates recovered from different specimens of nonmigratory bats (Artibeus hirsutus) captured in a cave in Morelos, by 5 isolates recovered from infected migratory bats (Leptonycteris nivalis) captured in Morelos and Puebla, and by 1 isolate from another migratory bat (L. curasoae) captured in Oaxaca. This polymorphic DNA pattern of H. capsulatum could represent fungal markers for the geographic areas studied, and considering its distribution in three different states of the Mexican Republic, the role of bats as responsible for H. capsulatum spreading in nature, in relation to their movements and migrations besides their shelter habits, is suggested. Analyses of DNA patterns of H. capsulatum isolated from infected bats, from clinical cases, and from blackbird excreta, have shown a major relatedness between bats and clinical isolates, in contrast to those isolates from bird excreta.

Animals↗
PubMed2005

Epidemiological study of invasive pulmonary aspergillosis in a haematology unit by molecular typing of environmental and patient isolates of Aspergillus fumigatus.

In order to determine the possible relationship between environmental contamination by Aspergillus fumigatus and occurrence of invasive aspergillosis, a one-year prospective study was carried out in the haematology ward of Hautepierre Hospital, Strasbourg, France. During the study period, 21 environmental isolates and 26 clinical isolates of A. fumigatus were collected. Each was genotyped using a random amplification of polymorphic DNA (RAPD) technique. Thirty-four distinct profiles were identified by RAPD analysis, indicating the great genetic diversity of A. fumigatus isolated from infected patients and from the environment. For two patients, RAPD analysis demonstrated concurrent infection by at least two different strains. In two cases, a genetic similarity was noted between isolates obtained from a patient and from the environment.

Air Microbiology↗
PubMed1997

Identification and DNA fingerprinting of Legionella strains by randomly amplified polymorphic DNA analysis.

The randomly amplified polymorphic DNA (RAPD) technique was used in the development of a fingerprinting (typing) and identification protocol for Legionella strains. Twenty decamer random oligonucleotide primers were screened for their discriminatory abilities. Two candidate primers were selected. By using a combination of these primers, RAPD analysis allowed for the differentiation between all different species, between the serogroups, and further differentiation between subtypes of the same serogroup. The usefulness of RAPD analysis was also evaluated with outbreak-related clinical and environmental isolates previously typed by the restriction fragment length polymorphism technique. RAPD analysis proved to be as accurate as other genotypic methods, reproducible, and highly discriminatory and is a valuable new alternative to traditional fingerprinting and identification of Legionella species and strains.

Animals↗