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Results for “Random Amplified Polymorphic DNA Technique”

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PubMed1999

Isolation of Acinetobacter spp. including A. baumannii from vegetables: implications for hospital-acquired infections.

A. baumannii is rarely recovered from the skin of patients or healthy European subjects as other genospecies predominate, but it isa significant nosocomial pathogen. The natural reservoir of this organism is therefore uncertain. We determined the isolation rates of Acinetobacter spp. from vegetables (as an indicator of the natural environment) using a selective technique and classified the genospecies by amplified ribosomal DNA restriction analysis (ARDRA). Of the 177 samples of vegetables examined, 30 yielded Acinetobacter, with genospecies 2 and 11 being the most common, each with a frequency of 27%. MIC assays showed that strains of genospecies 1, 2, 3, and 13TU (the A. calcoaceticus-A. baumannii complex) were significantly more resistant than other genospecies to ciprofloxacin and gentamicin. Vegetables may therefore be a natural habitat of A. baumannii and provide a route by which these bacteria are introduced into hospitals with obvious implications for infection control.

Acinetobacter↗

PubMed2002

Genetic diversity among Geotrichum candidum strains from various substrates studied using RAM and RAPD-PCR.

AIMS: Assessment of genetic diversity within the species Geotrichum candidum and development of tools to trace the strains that play an important role in the agro food industry. METHODS AND RESULTS: RAM-PCR and RAPD-PCR techniques were assessed for their ability to discriminate 57 strains of various morphotypes, substrates and geographical origin. The techniques were complementary and, when combined, allowed us to discriminate isolates. Moreover, we established a link between a taxon and its occupation of an ecological niche, which should not be confused with the substrate of isolation. CONCLUSIONS: We observed a high degree of diversity, which could be linked to the variety of the ecological niches chosen and to the high degree of morphological polymorphism encountered within the species. SIGNIFICANCE AND IMPACT OF THE STUDY: Used in combination, RAM-PCR and RAPD-PCR permit traceability and monitoring systems for G. candidum strains during food processing.

Animals↗

PubMed2003

[Application of ISSR technology in genetic diversity detection of jute].

The genetic diversity among 27 accessions of Corchorus, including 10 Jute species, was investigated with ISSR technique. 283 DNA bands were amplified with 25 ISSR primers, among which, 263 (92.85%) were polymorphic, with 10.48 bands per primer in average. A further systemic cluster analysis indicated that the accessions could be clustered into three groups, and the group II (including two cultispecies and their close wild species) was obviously genetically different from the groups I and III (including eight wild species). Moreover, 16 accessions in group II presented a higher intraspecific genetic resemblance, while 11 accessions among groups I & III showed an abundant interspecific genetic diversity. After synthesized the relevant findings of morphology and DNA classification, it's found that C. urticifolius could be one of the original wild species, C. tilaculariszic was a variation of C. tilaculari, and Tian Jute could be an untitled wild species.

DNA Fingerprinting↗

PubMed1995

Arbitrarily amplified DNA in systematics and phylogenetics.

Different polymerase chain reaction (PCR) based techniques which use single primers of arbitrary sequence have become prominent and powerful tools for taxonomic and genealogical studies. While the use of arbitrarily amplified DNA (AAD) markers for the identification of lower taxonomic units (e.g. at the species level) has been proven to be more or less straightforward, their potential usefulness in phylogenetic studies has not been sufficiently addressed yet. The main advantages of AAD markers include that they require only very small amounts of DNA, no sequence information of the taxa under investigation and the relative ease of the generating high numbers of AAD markers in short time. On the other hand, the generation of AAD markers is susceptible to certain random and systematic errors, and for phylogenetic studies the taxonomic level at which informative markers can be generated is severely limited.

Animals↗

PubMed1997

Genomic identification of Anisakis simplex isolates.

RAPD technique was used to differentiate individuals of Anisakis simplex obtained from Merluccius merluccius, Phycis blennoides, Conger conger and Lepidorhombus boscii, from the North Atlantic Ocean. The amplification patterns of the host DNA controls were markedly different from those obtained for the parasitic material. No variation within the same host was detected. The amplification patterns for larvae obtained from fish of the same genus were somewhat different. The amplification patterns of A. simplex isolates from M. merluccius, P. blennoides, C. conger and L. boscii, were different. These results suggest the possible existence of two populations with a considerable high genetic variability and a different adaptation to different host species.

Animals↗

PubMed2004

Phenotypic and genotypic identification of Candida spp. isolated from hospitalized patients.

As candidosis incidence continue to rise, quick laboratory identification of Candida species is becoming increasingly important for a growing population of patients at-risk. RAPD techniques were used on samples of Candida obtained from patients hospitalized at Santa Casa de Misericordia in Belo Horizonte (SCMBH) Brazil, from March 1998 to December 2000 and then compared with the results of phenotypic identification techniques. Two hundred and forty two yeasts were isolated and phenotypically identified as follows: Candida albicans (105), Candida tropicalis (62), Candida parapsilosis (28), Candida glabrata (19), Candida krusei (8), Candida guilliermondii (5) and Candida spp. (15). Samples from the three most frequent species isolated were selected randomly in order to compare the phenotypic and genotypic analyses. Genotypic analysis using RAPD primer M13 (F/R) displayed the best results of all test samples. There was both agreement and consistency between phenotypic and genotypic analysis using RAPD, demonstrating that is possible to apply this method for the identification of Candida species.

Candida↗

PubMed2003

Karyotypic and molecular identification of laboratory stocks of the South American fruit fly Anastrepha fraterculus (Wied) (Diptera: Tephritidae).

The taxonomic status of the tephritid pest Anastrepha fraterculus (Wied.) is a controversial subject, mainly because of misinterpretation of the observed genetic variation. In this work, the different karyotypes and DNA polymorphism of a geographically defined population from Northeastern Argentina were studied, using derived stocks maintained in the laboratory during 25 generations. The karyotypes were analyzed using C-banding and N-banding techniques, while DNA analysis was performed through the DNA polymerase chain reaction (PCR). The variants isolated from both the wild Montecarlo population and the derived laboratory stocks were fully compatible and are present in other wild populations from South Brazil (lat 31 degrees 30' S) to Mid-Argentina (lat 34 degrees 30' S). Single-pair crosses among stocks carrying different chromosomal variants demonstrated the absence of isolation barriers. The polymorphic fragments isolated by RAPDs/PCR showed polymorphisms among stocks whereas the analysis of rDNA ITS1 exhibit a unique ITS1 length. Our results seem to indicate that all the examined variants belong to a single species with extended polymorphism and therefore do not support the hypothesis that the extended chromosomal polymorphism in A. fraterculus implies the existence of a complex of cryptic species.

Animals↗

PubMed2003

Molecular cloning and nucleotide sequence analysis of encoded anti-insect toxin BotIT2 from the scorpion Buthus occitanus tunetanus venom.

Numerous toxins from scorpion venoms are much more toxic to insects than to other animal classes, and possess high affinity to Na+ channels. Many of them active on insects were purified from the venom of Buthus occitanus tunetanus. Using amino acid sequences of BotIT2 and RACE-PCR amplification (Rapid amplification of cDNA ends) technique, we isolated, identified and sequenced the nucleotide sequence from the venom glands of the scorpion Buthus occitanus tunetanus. The cDNA encodes a precursor of an insect toxin of 60 amino acid residues. The deduced nucleotide sequence toxin was identical to the determined amino acid sequence of BotIT2. BotIT2 is more similar to the excitatory toxins in its mode of action and to the depressant toxins in its primary structure.

Amino Acid Sequence↗

PubMed2000

Mycoplasmal conjunctivitis in songbirds from New York.

A field study was conducted to determine the prevalence of conjunctivitis and Mycoplasma gallisepticum (MG) infections in house finches (Carpodacus mexicanus) and other songbirds common to bird feeders in Tompkins County (New York, USA). Eight hundred two individuals of 23 species and nine families of birds were captured and given physical examinations during the 14 mo study beginning in February 1998. Clinical conjunctivitis (eyelid or conjunctival swelling, erythema, and discharge) was observed in 10% (19/196) of house finches examined, and only in the winter months from November to March. Unilateral conjunctivitis was observed in 79% (15/19) of affected house finches; one case developed bilateral disease between 8 and 18 days following initial examination. Conjunctivitis was observed in a similar proportion of males and females sampled, and body condition scores and wing chord lengths were not significantly different between diseased and non-diseased house finches. Mycoplasma gallisepticum was isolated from 76% (13/17) of finches with conjunctivitis and 2% (3/168) of clinically normal house finches sampled during the study. DNA fingerprints of 11 MG isolates using random amplification of polymorphic DNA (RAPD) techniques showed no apparent differences in banding patterns over the course of the study, suggesting persistence of a single MG strain in the study population. The prevalence of conjunctivitis and MG infections declined in house finches between February/March 1998 and February/March 1999 (23% to 6%, and 20% to 5%, respectively), but only the former was significant (P < 0.05). Conjunctivitis was also observed in four American goldfinches (Carduelis tristis) and one purple finch (Carpodacus purpureus). Mycoplasma gallisepticum infection was confirmed in the purple finch, the first documented case of MG-associated conjunctivitis in this species. The purple finch isolate was similar to house finch isolates from the study site by RAPD analysis. Positive plate agglutination (PA) tests were recorded in one other goldfinch and two purple finches, suggesting exposure of these individuals to MG. Positive PA tests were also obtained from two brown-headed cowbirds (Molothrus ater) and four tufted titmice (Parus bicolor), but MG infection could not be confirmed in these cases due to lack of samples. Based on these findings, the prevalence of MG infections in hosts other than house finches appear to be low in the population sampled. There is growing evidence, however, that songbird species other than house finches are susceptible to MG infection and disease.

Animals↗

PubMed1998

Intercontinental spread of a multidrug-resistant methicillin-resistant Staphylococcus aureus clone.

Two hundred ten methicillin-resistant Staphylococcus aureus (MRSA) isolates recovered between 1990 and 1997 from three Portuguese hospitals located in Lisbon and Oporto were analyzed by molecular fingerprinting techniques. The hybridization of ClaI restriction digests with the mecA- and Tn554-specific DNA probes combined with pulsed-field gel electrophoresis documented the abrupt appearance and extensive intrahospital spread of the Brazilian epidemic MRSA clone in the 1995 samples of each one of the three hospitals analyzed-suggesting the intercontinental transfer of this strain from Brazil to Portugal. The appearance of this clone may challenge the dominance of another highly epidemic imported clone-the Iberian MRSA, currently the most widely spread MRSA clone in Portuguese hospitals.

Brazil↗

PubMed2002

Molecular research on the genetic diversity of Polish varieties and landraces of Phaseolus coccineus L. and Phaseolus vulgaris L. using the RAPD and AFLP methods.

The aim of our research was to evaluate the genetic diversity among 25 commercial varieties registered in Poland and 14 landraces of Phaseolus vulgaris var. nanus Asch. (the dwarf common bean) and Phaseolus coccineus L. (the runner bean) maintained in the National Centre of Plant Genetic Resources in Radzików. An additional goal of this study was to compare the precision and efficiency of two techniques of PCR (RAPD and AFLP), used to estimation the genetic diversity of bean. The breeding varieties of bean were registered in the period between 1950 and 2000. The landraces, collected during expeditions conducted from 1985 to 1988, mainly originated from the eastern and southern part of Poland. In the plant genetic diversity research of RAPD and AFLP markers are commonly used. Complex electrophoresis pictures of DNA fragments were taken, and revealed a considerable polymorphism. The polymorphic fragments were obtained on the basis of 6 differentiating primers using the RAPD method and 15 differentiating primers using the AFLP method. P. vulgaris and P. coccineus accessions formed distinct groups. Each of the RAPD and AFLP analyses allowed for the unique distinguishing of all accessions.

Base Sequence↗

PubMed2005

Testing of amplified fragment length polymorphism (AFLP) technique as a tool for molecular epidemiology of Trichinella nativa.

A total of nine Trichinella nativa isolates were compared by amplified fragment length polymorphism (AFLP). Four hundred nanograms of genomic DNA from a pool of 10--20 larvae were digested using HindIII and MseI restriction endonucleases. Of the 16 primer combinations initially tested, Hind-C and Mse-C primers showed rich polymorphism with approximately 40--90 bands in the range of 30--270 bp. Genetic similarities were estimated visually. AFLP provided discriminatory banding patterns and may therefore be used as a method for detecting variation in T. nativa populations. However, the heterogeneous patterns obtained from pooled samples emphasize the need for further development of the sampling and numerical analysis of the patterns for epidemiological and taxonomical interpretation.

Animals↗

PubMed2003

Analysis of eggplant ( Solanum melongena)-related germplasm: morphological and AFLP data contribute to phylogenetic interpretations and germplasm utilization.

A total of 94 Solanum accessions, including eggplants and related species, were morphologically characterized based on greenhouse observations, and molecularly analysed by the AFLP technique. Morphological parameters were helpful in assessing similarities or differences among accessions, and molecular data were used to support morphological conclusions. A dendrogram was computed based on the Dice genetic distances using the neighbour-joining method. The analysis was efficient in the assignment of a species name for eight out of nine accessions that were not previously classified, and revealed that 14 further accessions were misnamed in the collection originally received. The results indicate that the taxonomy of Solanum sections and subgenera including several species should be reconsidered. The AFLP technique was revealed as an efficient tool in determining genetic relationships among species. In general, morphological observations were consistent with molecular data, indicating that both approaches complemented to define the phylogenetic status of a large genus like Solanum. In terms of eggplant breeding, the molecular analysis of the Melongena complex, and of the other sections of the subgenus Leptostemonum, establishes useful germplasm relationships in the gene pool available for the genetic improvement of the cultivated species. The results we have provided highlight an urgent necessity to include molecular parameters in handling and characterizing the genebank-deposited germplasm related to cultivated crops.

Breeding↗

PubMed2003

Fine mapping of the rice thermo-sensitive genic male-sterile gene tms5.

AnnongS-1, a thermo-sensitive genic male-sterile (TGMS) rice line, has a new TGMS gene. Genetic analysis indicated that the sterility of AnnongS-1 was controlled by a single resessive gene named tms5. In our previous studies based on an F(2) population from the cross between AnnongS-1 and Nanjing11, tms5 was mapped on chromosome 2. Recently, a RIL (recombinant inbred line) population from the same cross was developed and used for the fine mapping of the tms5 gene. Molecular marker techniques combined with BSA (bulked segregant analysis) were used. As a result, two AFLP markers (AF10, AF8), one RAPD marker (RA4), one STS marker (C365-1), one CAPs marker (G227-1) and four SSR markers (RM279, RM492, RM327, RM324) were found to be closely linked to tms5 gene. The DNA sequences of the RFLP marker of C365 and G227 were found in GenBank, and on the basis of these sequences, many primers were designed to amplify the two parents and their RIL population plants. Finally, the tms5 gene was mapped between STS marker C365-1 and CAPs marker G227-1 at a distance of 1.04 cM from C365-1 and 2.08 cM from G227-1.

Chromosome Mapping↗

PubMed2004

Plant-like mating in an animal: sexual compatibility and allocation trade-offs in a simultaneous hermaphrodite with remote transfer of sperm.

The importance of sexual compatibility between mates has only recently been realized in zoological research into sexual selection, yet its study has been central to botanical research for many decades. The reproductive characteristics of remote mating, an absence of precopulatory mate screening, internal fertilization and embryonic brooding are shared between passively pollinated plants and a phylogenetically diverse group of sessile aquatic invertebrates. Here, we further characterize the sexual compatibility system of one such invertebrate, the colonial ascidian Diplosoma listerianum. All 66 reciprocal pairings of 12 genetic individuals were carried out. Fecundities of crosses varied widely and suggested a continuous scale of sexual compatibility. Of the 11 animals from the same population c. 40% of crosses were completely incompatible with a further c. 20% having obvious partial compatibility (reduced fecundity). We are unaware of other studies documenting such high levels of sexual incompatibility in unrelated individuals. RAPD fingerprinting was used to estimate relatedness among the 12 individuals after a known pedigree was successfully reconstructed to validate the technique. In contrast to previous results, no correlation between genetic similarity and sexual compatibility was detected. The blocking of many genotypes of sperm is expected to severely modify realized paternity away from 'fair raffle' expectations and probably reduce levels of intra-brood genetic diversity in this obligatorily promiscuous mating system. One adaptive benefit may be to reduce the bombardment of the female reproductive system by outcrossed sperm with conflicting evolutionary interests, so as to maintain female control of somatic : gametic investment.

Animals↗

PubMed2006

Identification of AFLP markers linked to the male fertility restorer gene of CMS (Moricandia arvensis) Brassica juncea and conversion to SCAR marker.

We have developed a cytoplasmic male sterile (CMS) line of Brassica juncea through somatic hybridization with Moricandia arvensis and introgressed the fertility restorer gene into B. juncea. This fertility restorer locus is unique in that it is capable of restoring male fertility to two other alloplasmic CMS systems of B. juncea. As a first step toward cloning of this restorer gene we attempted molecular tagging of the Rf locus using the amplified fragment length polymorphism (AFLP) technique. A BC(1)F(1) population segregating for male sterility/fertility was used for tagging using the bulk segregant analysis method. Out of 64 primer combinations tested in the bulks, 5 combinations gave polymorphic amplification patterns. Further testing of these primers in individual plants showed four amplicons associated with the male fertility trait. Polymorphic amplicons were cloned and used for designing SCAR primers. One of the SCAR primers generated amplicons mostly in the fertile plants. Linkage analysis using MAPMAKER showed two AFLP and one SCAR markers linked to the male fertility gene with a map distance ranging from 0.6 to 2.9 cM. All the markers are located on one side of the Rf locus.

Fertility↗

PubMedDate not supplied

[The influence of chronic and of acute irradiation on the polymorphism of RAPD-markers in offspring for irradiated mice].

On mice lines BALB/c and CBA/lac was performed the study of molecular-genetics effects in mice progeny after the chronic (dose rate -0.0017 Gy/day, total dose -0.36 Gy) and acute (dose range 1-3 Gy) exposure of y-radiation on the parents. For variability analysis was used technique of amplification DNA with series of random primers (RAPD-assay). Random primers were used as single primer and in mixture of ones. In this work were held the comparative analysis of the genetic radiosensitivity for stem spermatogonia and spermatides. After the acute exposure the dose dependence for levels of polymorphism of RAPD-markers were obtained. After the chronic irradiation, significant differences from control group were obtained only by use primers mixture M1. Comparative analysis of the genetic radiosensitivity of different stages of mice spermatogenesis are display is similar sensitivity of stem spermatogonia and spermatides after doses of irradiation 1 Gy and 3 Gy. Indicated that after irradiation by dose 2 Gy, spermatogonia are more sensitivity than spermatides.

Animals↗

PubMed1998

Characterization and discrimination of three Theileria parva stabilates involved in East Coast fever vaccination.

Three vaccine stabilates of Theileria parva, of which sporozoites are being used against East Coast fever, were characterized by immunological and molecular biology techniques before being used for a national vaccination campaign in Kenya. T. parva Marikebuni stabilates 316 and 3014, and T. parva Lanet were used in this study and were discriminated from other Kenyan field Theileria isolates. IFAT results showed that all the animals were producing antibodies regardless of the stock used. Primers designed on the TPR1 gene sequence were used for PCR and Decamers were used for RAPD. Specific DNA band patterns (1,877 bp; 1,059 bp, and 443 bp) for the three vaccine stocks were observed. These molecular markers could be used to trace vaccinated animals in Kenya and to identify which isolates are responsible for reactions in animals.

Animals↗