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PubMed2001

Evaluation of PCR-restriction profile analysis and IS2404 restriction fragment length polymorphism and amplified fragment length polymorphism fingerprinting for identification and typing of Mycobacterium ulcerans and M. marinum.

Mycobacterium ulcerans and M. marinum are emerging necrotizing mycobacterial pathogens that reside in common reservoirs of infection and exhibit striking pathophysiological similarities. Furthermore, the interspecific taxonomic relationship between the two species is not clear as a result of the very high phylogenetic relatedness (i.e., >99.8% 16S rRNA sequence similarity), in contrast to only 25 to 47% DNA relatedness. To help understand the genotypic affiliation between these two closely related species, we performed a comparative analysis including PCR restriction profile analysis (PRPA), IS2404 restriction fragment length polymorphism (RFLP), and amplified fragment length polymorphism (AFLP) on a set of M. ulcerans (n = 29) and M. marinum (n = 28) strains recovered from different geographic origins. PRPA was based on a triple restriction of the 3' end region of 16S rRNA, which differentiated M. ulcerans into three types; however, the technique could not distinguish M. marinum from M. ulcerans isolates originating from South America and Southeast Asia. RFLP based on IS2404 produced six M. ulcerans types related to six geographic regions and did not produce any band with M. marinum, confirming the previous findings of Chemlal et al. (K. Chemlal, K. DeRidder, P. A. Fonteyne, W. M. Meyers, J. Swings, and F. Portaels, Am. J. Trop. Med. Hyg. 64:270-273, 2001). AFLP analysis resulted in profiles which grouped M. ulcerans and M. marinum into two separate clusters. The numerical analysis also revealed subgroups among the M. marinum and M. ulcerans isolates. In conclusion, PRPA appears to provide a rapid method for differentiating the African M. ulcerans type from other geographical types but is unsuitable for interspecific differentiation of M. marinum and M. ulcerans. In comparison, whole- genome techniques such as IS 2404-RFLP and AFLP appear to be far more useful in discriminating between M. marinum and M. ulcerans, and may thus be promising molecular tools for the differential diagnosis of infections caused by these two species.

Animals↗

PubMed2005

Molecular identification of Capnocytophaga spp. via 16S rRNA PCR-restriction fragment length polymorphism analysis.

Capnocytophaga spp. have been implicated as putative periodontal pathogens associated with various periodontal diseases. Although the genus is known to contain five human oral isolates, accurate identification to species level of these organisms recovered from subgingival plaque has been hampered by the lack of a reliable method. Hence, most studies to date have reported these isolates as Capnocytophaga spp. Previous attempts at identification were based on biochemical tests; however, the results were inconclusive. Considering the differing virulence features of the respective isolates, it is crucial to identify these isolates to species level. The universal and conservative nature of the 16S rRNA gene has provided an accurate method for bacterial identification. The aim of this study was to identify Capnocytophaga spp. via restriction enzyme analysis of this gene (16S rRNA PCR-restriction fragment length polymorphism). The results (backed up by 16S rRNA gene sequencing) showed that this method reliably identifies all named Capnocytophaga spp. to species level.

Bacterial Typing Techniques↗

PubMed1991

Restriction fragment length polymorphism of the L-myc gene and susceptibility to metastasis in genitourinary cancers.

We examined Southern blot analysis of genomic DNAs from 70 patients with sporadic renal cell carcinoma, using the human L-myc oncogene fragment as a hybridization probe. Our purpose was to study the relationship between the restriction fragment length polymorphism (RFLP) of the L-myc and the frequencies of metastasis. The patients were classified into 3 genotypes according to the polymorphic patterns defined by two alleles (L-L:17, L-S:31, S-S:22). The relative ratios of the 3 genotypes in the renal cancer patients were similar to those seen in healthy Japanese. However, of 20 patients who exhibited distant metastases at diagnosis, only 2 belonged to the L-L type. The incidence of distant metastasis in L-L type patients was significantly lower than that in L-S and S-S patients (p = 0.068, by Fisher's exact probability test). These results basically correspond to the previous findings in the lung cancer patients [Kawashima et al.: Proc. natn. Acad. Sci. USA 85: 2353-2356, 1988]. On the other hand, L-myc RFLP analysis in 50 prostatic cancer patients revealed that the incidence of metastasis at diagnosis did not correlate with L-myc genotypes. L-myc RFLP seems to be less promising in prostatic cancer than in lung or kidney cancer.

Blotting, Southern↗

PubMed1999

Genetic variation of Cryphonectria hypoviruses (CHV1) in Europe, assessed using restriction fragment length polymorphism (RFLP) markers.

A total of 72 hypovirus-infected isolates of the chestnut blight fungus Cryphonectria parasitica were sampled from nine European countries between 1975 and 1997. The double-stranded RNA of the Cryphonectria hypoviruses (CHV1) was isolated and reverse transcription (RT)-PCR products were obtained for two different regions of the viral genome (ORF A and ORF B) using primer sequences of the type species CHV1-EP713. Both PCR products of each viral isolate were digested with four restriction endonucleases recognizing sequences of four nucleotides. The restriction fragment length polymorphism (RFLP) analysis revealed 41 genetically distinct RFLP types of CHV1 with 10 types occurring more than once. Identical RFLP types were detected nine times among viruses collected in the same location. Cluster analysis based on the RFLP banding patterns separated the viral isolates into five CHV1 clusters or subtypes. Most viral isolates (64 out of 72) grouped into one large cluster which comprised all viruses from Italy (including CHV1-EP747), Switzerland, Crotia, Bosnia, Hungary, Greece, and the French island Corsica, as well as five out of 11 isolates from continental France. Two additional subtypes of CHV1 were found in France (one related to CHV1-EP713) and one each in Spain and Germany. The Swiss samples collected over a period of 20 years showed that very little RFLP variation has evolved during this time. The results of this study are consistent with the hypothesis of multiple introductions of CHV1 into Europe.

Ascomycota↗

PubMed2004

New method of differentiating wild-type varicella-zoster virus (VZV) strains from Oka varicella vaccine strain by VZV ORF 6-based PCR and restriction fragment length polymorphism analysis.

A new method was developed to distinguish accurately wild-type varicella-zoster virus (VZV) strains from the Oka vaccine strain. Several DNA fragments covering open reading frame (ORF) 1-37 were amplified from wild-type VZV strains including the Oka parent strain and from the Oka vaccine strain. Restriction fragment length polymorphisms of these regions were compared, and nucleotide differences between the vaccine virus and other wild-type VZV strains were noted in ORFs 6, 10, and 35. In addition, variations of the R2 and R4 reiterated structures of the vaccine and its parent strains were examined. The Oka vaccine strain used in Japan was shown to be a mixture of viruses with different nucleotide sequences that had variations in at least three nucleotide positions in ORF 1-37 and had variable polymorphisms at R2 and R4 repeat regions (two and three patterns, respectively). The Oka parent strain on the other hand showed a single sequence and had only one reiterated structure at these regions. When VZV ORF 6 was amplified and its product was digested with AluI, the Oka vaccine strain could be precisely differentiated from its parent and from 56 other Japanese clinical isolates.

Chickenpox Vaccine↗

PubMed1987

Restriction fragment length polymorphism of the C1 inhibitor gene in hereditary angioneurotic edema.

Hereditary angioneurotic edema (HANE) results from the deficiency of the inhibitor of the first component of human complement (C1-INH). It is inherited as an autosomal dominant trait. Heterogeneity of this defect has been shown at the protein and mRNA level. Southern blot analysis of genomic DNA was performed after digestion with six different restriction endonucleases in 24 families affected with type 1 HANE (low antigenic and functional C1-INH levels) and five with type 2 (low functional C1-INH levels and normal or elevated levels of dysmorphic C1-INH). Blots were hybridized with a C1-INH cDNA probe of 1,227 bp. With one enzyme (Pst I), two different patterns of restriction fragment length polymorphism (RFLP) were detected. One was present in one kindred with type 1 HANE and the other appeared the same in one type 1 and in one type 2 family, thus indicating that each RFLP resulted from a different mutation. Analysis of a total of 34 members of these three families suggested that the polymorphisms are tightly linked to the mutation responsible for the disease. Using a 170-bp probe we showed that the three different mutations leading to these polymorphisms are located in the same region of the C1-INH gene. These data suggest that different mutations in the same region of the C1-INH gene are responsible for C1-INH deficiency in these families. Most of these mutations are probably point mutations or other "minor" defects and do not appear to be due to major deletions or rearrangements.

Angioedema↗

PubMed1991

Prenatal diagnosis of Duchenne muscular dystrophy by restriction fragment length polymorphism analysis with pERT 87 intragenomic deoxyribonucleic acid probes.

Prenatal diagnosis of DMD was performed with three intragenic genomic probes and chorionic villus sampling. A total of 8 unrelated families with at least one DMD were analysed. DNA was extracted from peripheral white blood cells for carrier testings (50 individuals). For prenatal detection, it was extracted from chorionic villi obtained by chorionic villus sampling at 9 menstrual weeks. DNA was digested with an appropriate restriction enzyme followed by overnight electrophoresis in 1% agarose gels. DNA was transferred from the gel to nylon membrane according to the protocol of an alkaline transfer method. The pERT 87 probes were labeled by nick translation. The membranes were hybridized overnight after prehybridization. After washing, the membranes were exposed to X-ray films to make autoradiograms for restriction fragment length polymorphism analysis. Fetal sex was determined by a rapid screening test with a Y chromosome-specific repeat sequence. Out of 8 fetuses, 4 were males and 4 were females. All of 4 male fetuses were determined to be unaffected. Out of 4 female fetuses, 3 were diagnosed as non-carriers, and the carrier status of the remaining one was not able to be determined because her mother was not informative for all testings.

Chorionic Villi Sampling↗

PubMed1993

Genetic evidence for the existence of cryptic species in the Anopheles albitarsis complex in Brazil: allozymes and mitochondrial DNA restriction fragment length polymorphisms.

Allozyme and mitochondrial DNA (mtDNA) restriction studies were undertaken to determine the extent of genetic divergence among field populations of Anopheles albitarsis in Brazil. Two sympatric species, An. deaneorum and An. marajoara, were identified in collections from Costa Marques (CM), Rondonia. Genetic evidence includes (1) the presence of two types of individuals, each with diagnostic allelic clusters (for Had-1, Pgi-1, Pep-1, Mpi-1, and Idh-1), (2) a deficiency of heterozygotes, and (3) characteristic mtDNA haplotypes. In addition, two allopatric cryptic species of An. marajoara were identified, one from Iguape (An. marajoara form IG), Sao Paulo state, and the other from the Island of Marajo (An. marajoara form MA). Though form IG and form-MA resemble form CM in wing spot morphology, they differ from it in diagnostic allozymes and mtDNA haplotypes. An. marajoara form CM had a higher variability (mean heterozygosity, H = 0.22, and percentage of polymorphic loci, P = 66.7) than did form IG and form MA (H = 0.08 in both, and P = 25.0 and 33.3, respectively). Form MA and form IG are genetically more similar to each other than both are to form CM. Based on wing morphology, estimates of F statistics, and genetic similarities, we propose that An. albitarsis in Brazil is a species complex. It comprises at least two morphologically distinguishable species: (1) An. deaneorum (currently one taxon) and (2) the An. marajoara species complex, which further consists of at least three cryptic forms, marajoara form MA, marajoara form IG, and marajoara form CM.

Alleles↗

PubMed1986

Immunoglobulin heavy chain switch region restriction fragment length polymorphisms are associated with renal disease.

We describe here, to our knowledge for the first time, associations between polymorphisms at the genomic DNA level in the immunoglobulin gene region and renal diseases which lead to chronic renal failure. Recent studies have shown that protein polymorphisms, present in immunoglobulin (Ig) heavy chains (Gm allotypes) are associated with certain forms of renal disease and with end stage renal failure per se. To investigate this association at the DNA level we have used probes which recognize Ig heavy chain genes and this report describes results obtained with one of these, the S mu switch region probe. With the restriction endonuclease Sst 1 (or the isoschizomer; Sac I) a number of restriction fragment length polymorphisms (RFLP) can be obtained which are recognized by this probe and there is a highly significant association between certain of these and renal disease. This is the first report of Ig switch region polymorphisms being associated with disease, yet our results suggest that S mu RFLP are more closely linked to renal disease than Ig protein polymorphisms.

Humans↗

PubMed1989

Restriction fragment length polymorphism of the L-myc gene and susceptibility to metastasis in renal cancer patients.

We examined Southern blot analyses of normal and tumor DNAs from 50 patients with sporadic renal cancer, using the human L-myc oncogene fragment as a hybridization probe. Our purpose was to study the relationship between the restriction fragment length polymorphism (RFLP) of the L-myc and the frequencies of metastases. There was no individual difference in patterns of L-myc RFLP between normal and tumor-tissue DNAs digested with EcoRI. The patients were classified into 3 genetic types according to the polymorphic patterns defined by the 2 alleles [10-kilobase (kb) and 6.6-kb fragments]. The relative ratios of the 3 genotypes in the renal cancer patients were similar to those seen in healthy Japanese. However, of 16 patients who exhibited distant organ metastases at the time of surgery, only one was a 10-kb fragment homozygote. The incidence of distant metastases in 10-kb homozygotes was significantly lower than that in 6.6-kb homozygotes plus heterozygotes (p = 0.06). These results basically correspond to the previous findings in the lung cancer patients, and suggest that L-myc RFLP is a widely applicable genetic marker to predict prognosis in cancer patients.

Adult↗

PubMed2000

Identification of Nile perch (Lates niloticus), grouper (Epinephelus guaza), and wreck fish (Polyprion americanus) by polymerase chain reaction-restriction fragment length polymorphism of a 12S rRNA gene fragment.

Restriction site analysis of polymerase chain reaction (PCR) products from a conserved region of the 12S rRNA gene has been used for the specific identification of Nile perch (Lates niloticus), grouper (Epinephelus guaza), and wreck fish (Polyprion americanus). Amplification of DNA isolated from muscle samples was carried out using a set of primers flanking a region of 436 bp from the mitochondrial 12S rRNA gene. Digestions of the PCR products with RsaI and Sau96I endonucleases, followed by agarose gel electrophoresis of the digested PCR products, yielded specific profiles that enabled direct identification of each species analyzed.

Animals↗

PubMed1996

Identification of novel cry-type genes from Bacillus thuringiensis strains on the basis of restriction fragment length polymorphism of the PCR-amplified DNA.

Two pairs of universal oligonucleotide primers were designed to probe the most conserved regions of all known cryI-type gene sequences so that the amplified PCR fragments of the DNA template from Bacillus thuringiensis strains may contain all possible cryI-type gene sequences. The restriction fragment length polymorphism (RFLP) patterns of the PCR-amplified fragments revealed that 14 distinct cry-type genes have been identified from 20 B. thuringiensis strains. Those cry-type genes included cryIA(a), cryIA(a), cryIA(b), cryIA(b), cryIA(c), cryIB, cryIC, cryIC, cryIC(b), cryID, cryIE, cryIF, cryIF, and cryIII (a dagger at the end of a gene designation indicates a novel cry-type gene determined by restriction mapping or DNA sequences). Among them, the sequences of cryIA(a), cryIA(b), cryIB, cryIC, cryIF, and cryIII were found to be different from the corresponding published cry gene sequences. Interestingly, five cry-type genes [cryIA(a)-, cryIB-, cryIC-, cryIC(b)-, and cryIF-type genes] and seven cry-type genes [cryIA(a)-, cryIA(b)-, cryIB-, cryIC-, cryIC(b)-, cryIF-, and cryIII-type genes] have been detected from B. thuringiensis subsp. morrisoni HD-12 and B. thuringiensis subsp. wuhanensis, respectively. Therefore, the PCR-RFLP typing system is a facile method to detect both known and novel cry genes existing in B. thuringiensis strains.

Bacillus thuringiensis↗

PubMed1994

Cloning, sequencing and restriction fragment length polymorphism analysis of a porcine cDNA for OCT2.

A full-length pig cDNA for the POU-domain protein OCT2 has been isolated and sequenced. The 478 amino acid-long reading frame in pig OCT2 is 97% identical to human OCT2A, indicating strong conservation of function for this immunoglobulin regulatory protein. To investigate the potential use of this cDNA for mapping and identifying linkage of OCT2 to economic traits, restriction fragment length polymorphism (RFLP) analysis was used to identify a TaqI polymorphism. A population of 60 unrelated animals, as well as multigenerational families, were typed for this RFLP and showed variability in several American and Chinese breeds. The TaqI polymorphism was also detected by a non-POU-domain OCT2 probe, demonstrating that this RFLP is located in the OCT2 gene. This result suggests that OCT2 is likely to be a single-copy gene in swine as seen in other mammals.

Animals↗

PubMed2006

Characterization of Erwinia amylovora strains from different host plants using repetitive-sequences PCR analysis, and restriction fragment length polymorphism and short-sequence DNA repeats of plasmid pEA29.

AIMS: The three main aims of the study were the assessment of the genetic relationship between a deviating Erwinia amylovora strain isolated from Amelanchier sp. (Maloideae) grown in Canada and other strains from Maloideae and Rosoideae, the investigation of the variability of the PstI fragment of the pEA29 plasmid using restriction fragment length polymorphism (RFLP) analysis and the determination of the number of short-sequence DNA repeats (SSR) by DNA sequence analysis in representative strains. METHODS AND RESULTS: Ninety-three strains obtained from 12 plant genera and different geographical locations were examined by repetitive-sequences PCR using Enterobacterial Repetitive Intergenic Consensus, BOX and Repetitive Extragenic Palindromic primer sets. Upon the unweighted pair group method with arithmetic mean analysis, a deviating strain from Amelanchier sp. was analysed using amplified ribosomal DNA restriction analysis (ARDRA) analysis and the sequencing of the 16S rDNA gene. This strain showed 99% similarity to other E. amylovora strains in the 16S gene and the same banding pattern with ARDRA. The RFLP analysis of pEA29 plasmid using MspI and Sau3A restriction enzymes showed a higher variability than that previously observed and no clear-cut grouping of the strains was possible. The number of SSR units reiterated two to 12 times. The strains obtained from pear orchards showing for the first time symptoms of fire blight had a low number of SSR units. CONCLUSIONS: The strains from Maloideae exhibit a wider genetic variability than previously thought. The RFLP analysis of a fragment of the pEA29 plasmid would not seem a reliable method for typing E. amylovora strains. A low number of SSR units was observed with first epidemics of fire blight. SIGNIFICANCE AND IMPACT OF THE STUDY: The current detection techniques are mainly based on the genetic similarities observed within the strains from the cultivated tree-fruit crops. For a more reliable detection of the fire blight pathogen also in wild and ornamentals Rosaceous plants the genetic features of deviating E. amylovora strains have to be studied in detail.

Culture Media↗

PubMed1991

The human transmembrane secretory component (poly-Ig receptor): molecular cloning, restriction fragment length polymorphism and chromosomal sublocalization.

The human transmembrane secretory component (SC) mediates glandular translocation of polymeric IgA and IgM into exocrine secretions. A 2898-bp cDNA clone, encoding the entire sequence of the human transmembrane SC, was isolated from a colonic adenocarcinoma cell line cDNA library. The deduced amino-acid sequence had a length of 764 residues and showed an overall similarity of 56% and 64% with the rabbit and rat counterpart, respectively. A restriction fragment length polymorphism (RFLP) was found with PvuII, revealing a two-alle RFLP with an autosomal codominant inheritance pattern and allele frequencies of 0.65 and 0.35. Southern blot analysis of human-rodent somatic hybrid panels, including hybrids with translocation chromosomes carrying different parts of chromosome 1, assigned the SC gene to 1q31-q42, thus confirming a previously reported provisional assignment.

Amino Acid Sequence↗

PubMed1998

Differentiation between porcine reproductive and respiratory syndrome virus isolates by restriction fragment length polymorphism of their ORFs 6 and 7 genes.

Three distinct antigenic profiles were identified by comparing the reactivities of 15 Canadian field isolates, the attenuated U.S. vaccine (Ingelvac MLV) strain and 2 European reference strains (Lelystad and Weybridge) of the porcine reproductive and respiratory syndrome virus (PRRSV) by indirect immunofluorescence with a set of 4 monoclonal antibodies to the nucleocapsid (N) protein and 2 other to the matrix (M) protein. In the present study, 9 Canadian isolates for which the sequences were determined appeared closely related to 2 U.S. reference strains (ATCC VR-2332 and ATCC VR-2385) with amino acid identities varying between 90 to 98% for the M and N proteins; substitutions in the nucleotide sequences were distributed randomly throughout the ORFs 6 and 7 genes, and most were 3rd base silent mutations. In comparison, more than 30% divergence was demonstrated with the Lelystad virus. Furthermore, differentiation between North American and European isolates, and between field isolates and the MLV strain could be achieved by cutting PCR-amplified products encompassing both ORFs 6 and 7 genes with 4 restriction endonucleases. When taken individually, BsaJI and AluI were the more appropriate restriction enzymes for distinguishing the vaccine strain from field isolates. The results obtained suggest that the restriction fragment length polymorphism of the genomic region covering the ORFs 6 and 7 genes may be a valuable tool to differentiate among PRRSV isolates.

Animals↗

PubMed1996

Serotyping of Chlamydia trachomatis from inclusion conjunctivitis by polymerase chain reaction and restriction fragment length polymorphism analysis.

A molecular biological method of detecting and serotyping Chlamydia trachomatis (C. trachomatis) directly from conjunctival specimens by polymerase chain reaction (PCR) was developed and applied to the diagnosis of inclusion conjunctivitis. We amplified 1.2 kbp DNA fragments of ompA gene from 15 reference strains of C. trachomatis by two-step PCR using two pairs of primers. Restriction fragment length polymorphism analysis using a combination of three endonucleases (HinfI, HindIII and HhaI) completely differentiated 13 of the 15 serovars; the exceptions were B and Ba. We then used this method for 18 strains of C. trachomatis isolated from Japanese patients with inclusion conjunctivitis, serotyping them into six groups: D (5/18), G (5/18), E (3/18), H (2/18), F (1/18), and K (1/18). In our comparison of cell culture isolation with PCR analysis of 38 conjunctival swabs from 35 patients in Sapporo with follicular conjunctivitis, 8 were positive in culture isolation and were also positive in two-step PCR. Twenty-five of 26 strains (the 18 isolated strains and 8 strains amplified by two-step PCR) were genotyped to D, G, H, E, F, and K. One isolated strain could not be identified. The C. trachomatis which causes inclusion conjunctivitis in Japan appears to have a distribution of serovars similar to that of the sexually transmitted diseases.

Adolescent↗

PubMed1991

Typing of human polyomavirus JC virus on the basis of restriction fragment length polymorphisms.

JC virus DNA clones from the urine of nonimmunosuppressed Japanese individuals regularly contain an archetypal regulatory sequence which may have generated various regulatory sequences of JC virus isolates from patients with progressive multifocal leukoencephalopathy (PML). In this study, we established 15 new clones from the urine of Dutch, German, and Taiwanese healthy volunteers and patients. Most of these clones contained regulatory sequences essentially identical to the archetypal regulatory sequence. These clones, along with two representative urine-derived clones in Japan and five clones from the brains of PML patients (four established in the United States and one established in Japan), were analyzed with a number of restriction enzymes. We found nine restriction fragment length polymorphisms by which all clones were classified into either of the two types, A and B. Type A contained only clones from the West, while type B contained some from the West and all from eastern Asia. Each type contained both urine-derived and PML-derived clones. Furthermore, there was a close relationship between some urine-derived clones and some PML-derived clones in restriction site mapping analysis. These findings support the adaptation hypothesis which has been postulated to explain the genesis of PML-type JC viruses.

Base Sequence↗