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Results for “Random Amplified Polymorphic DNA Technique”

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PubMed1999

Species-specific detection of hydrocarbon-utilizing bacteria.

Rapid detection and quantitative assessment of specific microbial species in environmental samples is desirable for monitoring changes in ecosystems and for tracking natural or introduced microbial species during bioremediation of contaminated sites. In the interests of developing rapid tests for hydrocarbon-degrading bacteria, species-specific PCR primer sets have been developed for Pseudomonas aeruginosa, Stentrophomonas (Xanthomonas) maltophilia, and Serratia marsescens. Highly variable regions of the 16S rRNA gene were used to design these primer sets. The amplification products of these primer sets have been verified and validated with hemi-nested PCR and with ligase chain reaction (LCR) techniques, and have been applied to the analyses of environmental water samples. These species-specific primer sets were also chosen to amplify in conjunction with a universal set of PCR primers chosen from highly conserved neighboring sequences in the same gene. These multiplex or competitive PCR procedures enable testing with an internal marker and/or the quantitative estimation of the relative proportion of the microbial community that any one of these species occupies. In addition, this universal PCR primer set amplified the same size amplicon from a wide spectrum of procaryotic and eucaryotic organisms and may have potential in earth biota analyses.

Base Sequence↗

PubMed1999

Linear SRY transcript in equine testis.

Employing a combination of reverse transcription-polymerase chain reaction (RT-PCR) and rapid amplification of cDNA ends (RACE) techniques, the complete coding sequence of cDNA for the equine SRY gene was determined. We also attempted to make clear whether the equine SRY gene transcript is expressed in the adult testis, and whether the type of transcript is expressed as linear or circular RNA. As a result, in total a 1420 bp cDNA sequence was determined. Accomplishment of 3' RACE infers that equine SRY gene was expressed as a linear RNA transcript in testicular tissue just after puberty, in contrast to the situation in mice.

Amino Acid Sequence↗

PubMed2001

Differentiation of Lactobacillus plantarum, L. pentosus and L. paraplantarum species by RAPD-PCR and AFLP.

Two high-resolution genotypic techniques (RAPD-PCR and AFLP) were evaluated for their possibility to discriminate the species Lactobacillus plantarum, Lactobacillus pentosus and Lactobacillus paraplantarum and to type these taxa at the infra-species level. In total 23 strains of L. plantarum, three strains of L. pentosus, two strains of L. paraplantarum and two related strains for which the species assignment was not clear, were studied. For RAPD-PCR, suitable oligonucleotides and amplification conditions were selected and tested. For AFLP, a double digest of total genomic DNA was used and a subset of restriction fragments was selectively amplified and visualised using different primer combinations. Both methodologies generated, species-specific electrophoretic profiles. Moreover, the presence of distinct subgroups was revealed within the species L. plantarum.

Cluster Analysis↗

PubMed1998

Alterations in cytochrome-c oxidase expression between praziquantel-resistant and susceptible strains of Schistosoma mansoni.

The genetic differences between praziquantel-resistant (R) and susceptible (S) strains of Schistosoma mansoni (Fallon & Doenhoff, 1994) were explored using RAPD and by cloning differentially expressed mRNAs by subtractive PCR. No differences between the 2 strains were detectable by RAPD using 41 different primers indicating that no major genomic rearrangements were present. Subtractive PCR generated a number of fragments, 1 of which was shown to correspond to an over-expressed mRNA in the R strain and to encode a fragment of the subunit 1 of cytochrome-c oxidase (SCOX1). In the absence of a complete sequence for this gene, we used EST sequences to compile a consensus sequence for the 904 bp at the 3' end that enabled us to choose primers for semi-quantitative RT-PCR. This technique showed that SCOX1 was indeed over-expressed about 5 to 10-fold in the R strain whereas the genes encoding the 28 kDa glutathione S-transferase, glutathione peroxidase, NADH dehydrogenase subunit 5 and the ATP-binding cassette family protein SMDR2 were not. In contrast, cytochrome-c oxidase enzyme activity was 4-fold lower in the R strain than in the S strain.

Amino Acid Sequence↗

PubMed2006

[Consanguinity of sixteen olethreutid moth species in northeast China based on RAPD-PCR analysis].

With RAPD-PCR technique, the phylogenetic tree of 16 olethreutid moth species in northeast China was constructed, and their consanguinity was analyzed. The results showed that the clustering of 3 Pandemis species,2 Argyrotaenia species and 4 Archips species on this phylogenetic tree was coincident with their morphological taxology, but that of some other species was not. For example, Clepsis rurinana and C. pallidana were not on the same clade, but on the clade with Pandemis cinnamomeana and Ptycholoma imitartor, respectively. Genetic distance could be an index for genus, and 0.7 was the boundary. The species genetic distance from the same genus was less than 0.7, while that from different genus was more than 0.7.

Animals↗

PubMed2005

Genetic typing of Malassezia pachydermatis from different domestic animals.

In the present study, random amplification of polymorphic DNA, which detects DNA polymorphism in fungal genomic DNA, was applied for genetic typing of Malassezia pachydermatis isolates. Fifty-five isolates from different domestic animals and body sites and the neotype strain CBS 1879 were characterized. Primers M13 and OPT-20 were used to analyse their genetic relatedness and similarity. This technique allowed us to distinguish four different genetic types. The predominant genetic type was observed in isolates recovered from different anatomical locations in all animals. It was the only genetic type found in cats, horse, goat and pig. The other three genetic types were observed only in isolates from external ear canals of dogs. Types II and IV were only recovered from external otitic ears and type III from healthy ears. An animal was colonised by more than one type of M. pachydermatis and different genetic types were detected in the same body site. Some genetic types were only isolated from diseased skin.

Animals↗

PubMed2006

Biogeography of Brazilian populations of Panstrongylus megistus (Hemiptera, Reduviidae, Triatominae) based on molecular marker and paleo-vegetational data.

In epidemiological terms, Panstrongylus megistus is one of the most important species of triatomine bug in Brazil. Samples from 11 localities were studied using the random amplification of polymorphic DNA (RAPD) technique, which was able to differentiate the study populations clearly. Biogeographical data indicate that these populations could already have arisen 18,000 years ago (C(14)), it being possible to differentiate insects from the Brazilian states of Santa Catarina (SC) in the south, Ceará (CE) in the northeast and another large intermediate block containing the remaining eight populations from five other states. These results agree with those obtained by phenograms constructed from RAPD data, in which the SC population lies opposite those of CE, consistent with the greatest geographical distance between these localities. The other eight populations (Alagoas (AL), Bahia (BA), Goiás (GO), Minas Gerais (MG) and São Paulo (SP)) are closer genetically and originated in areas whose vegetational characteristics have remained similar to each other during the last 18,000 years, thus allowing greater contact between them. The greatest divergence of this group of insects and those of Ceará appears to have occurred 8000 years ago. This more humid period gave rise to other landscape changes, allowing greater differentiation of the vegetation and consequent expansion of P. megistus populations. Formation of the Serras do Mar and Mantiqueira probably created geographical barriers that favored a certain degree of isolation and greater differentiation of the SC population. Atlantic forest remnants within the caatinga domain (created between 25 and 17,000 years ago), where the CE populations originated probably constitute ecological refugia produced by successive amplification and retraction of the most suitable habitats for this species.

Animals↗

PubMed2000

[Isolation and sequence analysis of a mitochondrial DNA fragment associated with CMS in Hong Lian type rice].

A CMS line specific mtDNA band TA1 was isolated by comparing the mtDNAs of CMS line and maintainer line using AFLP technique. The Northern blot analysis of the TA1 mtDNA fragment show that it transcripts only one RNA molecular each in CMS line, maintain line and the first filial generation, but the RNA moleculars are different among each other. By sequencing, the fragment is found to be 202 base pairs in length. It contains code ATG, ATT, AGA and AGG, two small repeated sequences 5'TGTAC3' and 5'ATTATTTT3' and one small inverted-repeated sequence 5'GGGAAACA3'. The results imply that the mtDNA fragment may be a coding region and may be relative to CMS of Hong Lian type rice.

Base Sequence↗

PubMed2000

Safety assessment of potential probiotic lactic acid bacterial strains Lactobacillus rhamnosus HN001, Lb. acidophilus HN017, and Bifidobacterium lactis HN019 in BALB/c mice.

The general safety of immune-enhancing lactic acid bacteria (LAB) strains Lactobacillus rhamnosus HN001 (DR20), Lb. acidophilus HN017, and Bifidobacterium lactis HN019 (DR10) was investigated in a feeding trial. Groups of BALB/c mice were orally administered test LAB strains or the commercial reference strain Lb. acidophilus LA-1 at 2.5 x 10(9), 5 x 10(10) or 2.5 x 10(12) colony forming units (CFU)/kg body weight/day for 4 weeks. Throughout this time, their feed intake, water intake, and live body weight were monitored. At the end of the 4 week observation period, samples of blood, liver, spleen, kidney, mesenteric lymph nodes, and gut tissues (ileum, caecum, and colon) were collected to determine: haematological parameters (red blood cell and platelet counts, haemoglobin concentration, mean corpuscular volume, mean corpuscular haemoglobin, and mean corpuscular haemoglobin concentration); differential leukocyte counts; blood biochemistry (plasma total protein, albumin, cholesterol, and glucose); mucosal histology (epithelial cell height, mucosal thickness, and villus height); and bacterial translocation to extra-gut tissues (blood, liver, spleen, kidney and mesenteric lymph nodes). DNA finger printing techniques were used to identify any viable bacterial strains recovered from these tissues. The results demonstrated that 4 weeks consumption of these LAB strains had no adverse effects on animals' general health status, haematology, blood biochemistry, gut mucosal histology parameters, or the incidence of bacterial translocation. A few viable LAB cells were recovered from the tissues of animals in both control and test groups, but DNA fingerprinting did not identify any of these as the inoculated strains. The results obtained in this study suggest that the potentially probiotic LAB strains HN001, HN017, and HN019 are non-toxic for mice and are therefore likely to be safe for human use.

Animals↗

PubMed2001

Development of a method for mRNA differential display in filamentous fungi: comparison of mRNA differential display reverse transcription polymerase chain reaction and cDNA amplified fragment length polymorphism in Leptosphaeria maculans.

We modified a technique, cDNA-AFLP, for identifying differentially expressed genes in plants to work in the filamentous fungus Leptosphaeria maculans (Desmaz.) Ces. & De Not. The cDNA fragments generated by our method ranged in size from approximately 100 to 400 bps. On average, twice as many cDNA fragments were amplified per primer set with cDNA amplified fragment length polymorphism in comparison with mRNA differential display reverse transcription polymerase chain reaction. The DNA fragments of interest were excised from gels and analyzed by single-stranded conformation polymorphism to eliminate nondifferentially expressed cDNA contamination. The method was used to examine gene expression differences between cultures grown in the presence or absence of an analog of the Brassica phytoalexin brassinin. Eleven of the fourteen fragments examined were determined by reverse Northern blot to be differentially expressed. In examining gene expression differences between young cultures not producing sirodesmins and older cultures that were producing these phytotoxins, we found 17 of 25 fragments were differentially expressed. Northern blots with these fragments confirmed the results.

Ascomycota↗

PubMed2004

Detection and genetic distance of resistant populations of Pseudosuccinea columella (Mollusca: Lymnaeidae) to Fasciola hepatica (Trematoda: Digenea) using RAPD markers.

Twelve natural populations of Pseudosuccinea columella snails, sampled in the western and central regions of Cuba, were analyzed using the RAPD-PCR technique to screen for resistance to Fasciola hepatica. Ten OPA primers previously shown to produce marker bands for resistance and susceptibility were tested. A new population of P. columella (El Azufre, Pinar del Río) exhibited the amplification patterns of resistant snails, and its resistant status was confirmed after experimental exposure to miracidia. No genetic variability was detected across or within the susceptible isolates. Similarly, the novel resistant isolate displayed an RAPD profile identical to the profile of two other isolates previously identified as resistant to F. hepatica. However, clear differences in RAPD banding patterns and genetic distance were observed between resistant and susceptible isolates.

Animals↗

PubMed2004

[Rapid construction of full-length MnSOD cDNA of chickens by one-step 3'RACE].

RACE (rapid amplification of cDNA ends) is a popular technique to rapidly obtain the full-length cDNA. After obtaining the 3' cDNA and 5' cDNA fragments with a overlapped region by 3' RACE and 5' RACE, the full-length cDNA could be generated by end-to-end PCR or subcloning. In this study, 3' RACE combined with touch-down PCR was successfully used for the rapid construction of full-length MnSOD cDNA of chickens. Compared with the conventional end-to-end PCR or subcloning, this method, called one-step 3' RACE, is fast, economical and highly specific. It especially fits the rapid construction of full-length cDNA by RACE method.

Animals↗

PubMed2001

Differential gene expression in neutrophils from patients with generalized aggressive periodontitis.

Differential gene expression was investigated in neutrophils stimulated with N-formyl-methionyl-leucyl-phenylalanine using RNA fingerprinting by arbitrarily primed polymerase chain reaction (RAP-PCR). The cells were isolated from 3 groups of subjects: patients with generalized aggressive periodontitis (Aggressive-P. n = 6), generalized chronic periodontitis (Chronic-P, n = 6) and healthy controls (H, n = 8). Our results show that 37 genes were upregulated. while 27 genes were down-regulated in all Aggressive-P neutrophils by using RAP-PCR with 45 primer pairs. Reverse transcription-PCR analyses revealed that mRNA levels were significantly different (p<0.05) for heat shock transcription factor 4b (HSF4b) gene. Kruppel-like zinc finger transcription factor 9 (Zf9) and muskelin genes. HSF4b was greater in neutrophils from Aggressive-P compared to groups H and Chronic-P. Zf9 and muskelin genes were lower in Aggressive-P compared to the H groups, but no significant difference was noted compared to the Chronic-P group. The control genes, IL-1beta and VEGF genes, were expressed at a significantly higher level in Aggressive-P and Chronic-P than H (p<.01, p<0.05). In conclusion, the RAP-PCR technique used in this study enabled us to identify 3 Aggressive-P related genes, which had not been reported previously. Neutrophil functions in Aggressive-P patients are suggested to be altered by regulatory factors of the immune system including HSF4b (transcription factor), Zf9 (activator of TGF-beta) and muskelin (cellular adhesion).

Adult↗

PubMed2003

Comparative study of the discriminating capacity of RAPD, AFLP and SSR markers and of their effectiveness in establishing genetic relationships in olive.

RAPDs, AFLPs and SSRs were compared in terms of their informativeness and efficiency in a study of genetic diversity and relationships among 32 olive cultivars cultivated in Italy and Spain. SSRs presented a higher level of polymorphism and a greater information content, as assessed by the expected heterozygosity, than AFLPs and RAPDs. The lowest values of expected heterozygosity were obtained for AFLPs, which, nevertheless were the most efficient marker system due to their capacity to reveal the highest number of bands per reaction and because of the high values achieved for a considerable number of indexes. All three techniques discriminated the genotypes very effectively, but only SSRs were able to discriminate the cultivars Frantoio and Cellina. The correlation coefficients of similarity were statistically significant for all three marker systems used but were lower for the SSR data than for RAPDs and AFLPs. For all markers a high similarity in dendrogram topologies was obtained although some differences were observed. All the dendrograms, including that obtained by the combined use of all the marker data, reflect some relationships for most of the cultivars according to their geographic diffusion. AMOVA analysis detected greater genetic differentiation among cultivars within each country than it did between the two countries.

Genetic Markers↗

PubMed2004

The Mycobacterium tuberculosis Rv2358-furB operon is induced by zinc.

The Mycobacterium tuberculosis genome encodes two ferric uptake regulator homologues, furA and furB, the function of which is under investigation. Using Mycobacterium smegmatis as a model system, we investigated the transcriptional pattern of Rv(Ms)2358-furB genes. Transcripts covering the two genes could be identified by northern blotting and by reverse transcriptase PCR. The transcriptional start point was mapped at one base upstream of the Ms2358 start codon by the RACE technique. By cloning M. smegmatis and M. tuberculosis DNA regions upstream of a reporter gene, we demonstrated the presence of one promoter, located immediately upstream of the Rv(Ms)2358 gene. Promoter induction was tested on several cultures grown under different conditions of pH and temperature, and in the presence of different concentrations of metallic ions. The promoter was found to be specifically induced by zinc. The recombinant M. tuberculosis FurB protein typically contained two zinc ions per protein monomer. Complete removal of zinc could not be obtained, even with strong denaturation treatment. Our data are in favour of the hypothesis that Rv2358 and FurB are transcriptional regulators involved in zinc homeostasis.

Amino Acid Sequence↗

PubMed2005

Differential expression of chitin synthase (CHS) and glucan synthase (FKS) genes correlates with the formation of a modified, thinner cell wall in in vivo-produced Beauveria bassiana cells.

During infection (in vivo), the entomopathogenic fungus Beauveria bassiana produces yeast-like cells that are surrounded by modified cell walls. These modifications have been related to the fungus ability to limit recognition by the host defense system. The composition of the in vivo cell wall was analyzed using a combination of cytochemical and molecular techniques. The in vivo cell walls still contained both chitin and 1,3-beta-glucan, but they were significantly thinner than in vitro cell walls (50-60 nm versus 100-160 nm, respectively). The difference in cell wall thickness was correlated with transcriptional regulation of cell wall-related genes: quantitative RT-PCR reactions demonstrated that B. bassiana chitin synthase (CHS) and glucan synthase (FKS) genes are down regulated in vivo. These analyses indicate that in vivo-triggered phenotypic modifications, including cell wall adjustments, are controlled by molecular mechanisms that include regulation of gene expression at the transcriptional level.

Amino Acid Sequence↗

PubMed1996

Genetic heterogeneity in the Trypanosoma brucei gambiense genome analysed by random amplification of polymorphic DNA.

The random amplification of polymorphic DNA (RAPD) technique has the potential to produce large amounts of characterisation data very quickly and simply, using far less DNA than conventional restriction-fragment-length polymorphism (RFLP) analysis. In the present study we assessed genetic heterogeneity among 34 Trypanosoma brucei gambiense isolates from various endemic areas in Africa by the RAPD technique using 8 arbitrary primers and compared the results with those obtained previously from RFLP analysis of polymorphisms in 5 variant surface glycoprotein (VSG) genes. The isolates were compared both among themselves and with 3 T. b. non-gambiense isolates. Most of the primers produced RAPD profiles specific for T. b. gambiense, with 4 primers showing marked polymorphisms between T. b. gambiense and non-gambiense stocks. These primers also showed minor variations between the T. b. gambiense stocks, and 2 revealed differences between Cameroonian stocks. These results were comparable with those produced by RFLP analysis, where certain polymorphisms are characteristic of T. b. gambiense. Numerical analysis showed a high correlation between the RAPD and RFLP data, with genetic variation being detected at a finer level by RAPD analysis. We conclude that RAPD analysis provides a simple and accurate method for the characterisation of T. b. gambiense.

Animals↗

PubMed2006

Detection and characterization of Salmonella associated with tropical seafood.

The prevalence of Salmonella in seafood samples collected from the southwest coast of India was studied by conventional culture and by a DNA based molecular technique, polymerase chain reaction (PCR). While conventional culture techniques detected Salmonella in only 20 out of the 100 samples analyzed, direct enrichment lysate PCR detected 52 as positive for Salmonella. A set of three different PCR primers viz., hns, invA and invE were used. It was observed that hns primer detected Salmonella in a significantly higher number of samples. Fourteen out of nineteen isolates belonged to serovar S. enterica Weltevreden. S. Weltevreden isolates were genotyped yielding 4 different patterns both by RAPD and ERIC-PCR but when combined, the overall results discriminated the isolates of S. Weltevreden into 6 different types. This suggests that genetically diverse Salmonella Weltevreden are prevalent in seafood.

Animals↗