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PubMed1999

Identification of Bartonella species directly in clinical specimens by PCR-restriction fragment length polymorphism analysis of a 16S rRNA gene fragment.

It is now established that two species of Bartonella, namely, Bartonella henselae and B. quintana, cause bacillary angiomatosis in human immunodeficiency virus-infected patients. In addition, B. henselae causes cat scratch disease and B. quintana, B. henselae, and B. elizabethae can cause bacteremia and endocarditis in immunocompetent persons. We have developed a PCR-restriction fragment length polymorphism-based assay for direct detection and identification to species level of Bartonella in clinical specimens. This is accomplished by PCR amplification of Bartonella DNA using primers derived from conserved regions of the gene carrying the 16S ribosomal DNA, followed by restriction analysis using DdeI and MseI restriction endonucleases. We amplified a Bartonella genus-specific 296-bp fragment from 25 clinical samples obtained from 25 different individuals. Restriction analysis of amplicons showed that identical patterns were seen from digestion of B. henselae and B. quintana amplicons with DdeI, whereas a different unique pattern was seen by using the same enzyme with B. vinsonii and B. elizabethae. With MseI digestion, B. henselae and B. vinsonii gave nearly identical patterns while B. quintana and B. elizabethae gave a different pattern. By combining the restriction analysis data generated with MseI and DdeI, unique "signature" restriction patterns characteristic for each species were obtained. These patterns were useful in identifying the Bartonella species associated with each tissue specimen.

Angiomatosis, Bacillary↗
PubMed2006

Trypanosoma evansi: genetic variability detected using amplified restriction fragment length polymorphism (AFLP) and random amplified polymorphic DNA (RAPD) analysis of Kenyan isolates.

We compared two methods to generate polymorphic markers to investigate the population genetics of Trypanosoma evansi; random amplified polymorphic DNA (RAPD) and amplified restriction fragment length polymorphism (AFLP) analyses. AFLP accessed many more polymorphisms than RAPD. Cluster analysis of the AFLP data showed that 12 T.evansi isolates were very similar ('type A') whereas 2 isolates differed substantially ('type B'). Type A isolates have been generally regarded as genetically identical but AFLP analysis was able to identify multiple differences between them and split the type A T. evansi isolates into two distinct clades.

Animals↗
PubMed1996

Restriction fragment length polymorphism of genes of the alpha 2(XI) collagen, bone morphogenetic protein-2, alkaline phosphatase, and tumor necrosis factor-alpha among patients with ossification of posterior longitudinal ligament and controls from the Japanese population.

STUDY DESIGN: The present study analyzed the restriction fragment length polymorphism patterns of alpha 2(XI) collagen, bone morphogenetic protein-2, alkaline phosphatase, and tumor necrosis factor-alpha genes in patients with ossification of the posterior longitudinal ligament. This study investigates the genetic polymorphism of bone-induced factors in patients with ossification of the posterior longitudinal ligament and compares it with healthy control subjects. OBJECTIVES: To clarify the genetic markers linked to ossification of the posterior longitudinal ligament. SUMMARY OF BACKGROUND DATA: Ossification of the posterior longitudinal ligament is a genetic disease associated with abnormal calcium metabolism involving the posterior longitudinal ligament. Previous genetic studies have not identified the pathologic mechanism of ossification of the posterior longitudinal ligament. Histopathologic studies of ossification of the posterior longitudinal ligament and the animal model, the spinal hyperostotic mouse, have revealed an increase in Type XI collagen and bone morphogenetic protein-2 expression. METHODS: Eighteen Japanese patients with ossification of the posterior longitudinal ligament and 51 healthy, unrelated control subjects were investigated for the restriction fragment length polymorphism patterns of COL11A2, bone morphogenetic protein-2, alkaline phosphatase, and tumor necrosis factor-alpha, genes with various restriction endonucleases. RESULTS: The gene frequencies of COL11A2 obtained with BamHl (10.0 kb fragment) and HindIII (19.0 kb fragment) observed in patients with ossification of the posterior longitudinal ligament were higher compared with control subjects (0.43 and 0.14, respectively). These differences were statistically significant (BamHl P = 0.018; Hindlll P = 0.046). Two new restriction fragment length polymorphism patterns were detected of the bone morphogenetic protein-2 gene with Mspl and Taql and one already known restriction fragment length polymorphism pattern of the tumor necrosis factor-alpha gene with Ncol. However, they were not significantly different from the control subjects. CONCLUSIONS: Seven restriction fragment length polymorphisms of COL11A2 gene were identified. Two of them (BamHl, 10.0/10.0 kb genotype; HindIII, 19.0/19.0 kb genotype) were significantly different in patients with ossification of the posterior longitudinal ligament.

Alkaline Phosphatase↗
PubMed2000

DNA fingerprints of Trichinella as revealed by restriction fragment length polymorphism and single-strand conformational polymorphism (RFLP-SSCP).

A method was developed for gene fingerprinting, combining the principles of restriction fragment length polymorphism and single-strand conformational polymorphism (PCR-RFLP-SSCP). Taking advantage of this method, we analysed the genotypes of 20 isolates from five species of Trichinella (Trichinella spiralis, Trichinella britovi, Trichinella nativa, Trichinella murrelli and Trichinella pseudospiralis) and two uncertain genotypes (Trichinella T6 and Trichinella T8). Target genes for the analysis included three kinds of random amplified polymorphic DNA (RAPD), the gene encoding 43 kDa excretory-secretory protein, the gene encoding mitochondrial cytochrome c -oxidase subunit I and the gene of 18 S rRNA. The genotype revealed by this method was in good concordance with the taxonomy of Trichinella (six species and two uncertain genotypes which is currently accepted based on morphology, isozyme pattern and reproductive isolation). More important, this method revealed intraspecies polymorphism among geographical isolates of T. spiralis and T. britovi.

Animals↗
PubMed2006

Rapid screening of fluoroquinolone resistance determinants in Streptococcus pneumoniae by PCR-restriction fragment length polymorphism and single-strand conformational polymorphism.

A rapid method, using PCR-restriction fragment length and single-strand conformation polymorphism (SSCP), was applied to screen for mutations of the fluoroquinolone resistance determinants in Streptococcus pneumoniae. One hundred nonduplicate Streptococcus pneumoniae isolates with ciprofloxacin MICs of > or = 4.0 microg/ml from the Prince of Wales Hospital, Hong Kong, years 2000 to 2003, were examined. For each isolate, PCR amplicons of quinolone resistance-determining regions (QRDRs) of gyrA, gyrB, parC, and parE genes were digested with AluI, HinfI, Sau3AI, and MspI, respectively, and analyzed by SSCP. Each SSCP pattern was given a number, and each isolate obtained a four-digit code, e.g., 1111, that represented the SSCP profile. The SSCP patterns were correlated to mutations characterized from sequence analyses of PCR amplicons. The most common SSCP profile obtained was no. 5232 (40%), which included strains with two amino acid substitutions in the ParC (Lys-137-Asn) and ParE (Ile-460-Val) genes, followed by the SSCP profile 5223 (17%), which included strains with amino acid substitutions in the ParE (Ile-460-Val) gene only. Ten isolates (10%) with amino acid substitutions at GyrA and ParE (+/-ParC) genes were resistant to levofloxacin with a MIC of > or = 16 microg/ml. Other SSCP profiles were unique in distinguishing the common amino acid substitutions in GyrA (Ser-81-Phe) and ParC (Lys-137-Asn, Ser-79-Phe plus Lys-137-Asn, Asp-83-Asn plus Lys-137-Asn, Ser-79-Phe, and Glu-96-Asp). SSCP analysis of restricted fragments generated patterns that were highly discriminative for mutations present in the QRDRs of gyrA, gyrB, parC, and parE. This method provides a database of high resolution profiles on these mutations and allows rapid screening for new mutations of the fluoroquinolone resistance genes.

Amino Acid Substitution↗
PubMed1988

Restriction-fragment-length polymorphism in insulin-receptor gene and insulin resistance in NIDDM.

Restriction-enzyme analysis of genomic DNA from 52 White and Hispanic nondiabetic subjects and 51 subjects with non-insulin-dependent diabetes (NIDDM) was carried out with insulin-receptor cDNA probes. A polymorphic 5.8-kilobase SstI fragment was found in 12 (23.5%) of 51 NIDDM subjects but only in 4 (7.7%) of 52 nondiabetic control subjects. This association is significant by chi 2-analysis (P less than .05). Furthermore, the nondiabetic subjects with the polymorphism were found to have hyperinsulinemia and/or nondiagnostic glucose tolerance. The polymorphism is a genetic marker for a phenotype that is neither necessary nor, by itself, sufficient for NIDDM. Nevertheless, it may indicate that insulin resistance functionally related to an insulin-receptor gene polymorphism is the proximal cause of NIDDM in at least one subset of the population.

Aged↗
PubMed1987

Globin gene-associated restriction-fragment-length polymorphisms in southern African peoples.

The combination of polymorphic restriction-enzyme sites in the 3' region of the beta-globin gene cluster shows very little variation in southern-African Bantu-speaking black and Kalahari !Kung San populations. The sites of the 5' region, on the other hand, show marked variation, and two common haplotypes are present--the "Negro" type (- - - - +) and the "San" type (- + - - +)--in frequencies of .404 and .106, respectively, in the Bantu-speakers and .262 and .405, respectively, in the San. Twenty of 23 beta s-associated haplotypes in southern-African Bantu-speaking black subjects were the same as that found commonly in the Central African Republic (CAR)--i.e., the "Bantu" type--a finding providing the first convincing biological evidence for the common ancestry of geographically widely separated speakers of languages belonging to the Bantu family. The (-alpha) haplotype has a frequency of .21 in the Venda, .07 in both the Sotho-Tswana and the Nguni, and .06 among the !Kung San. These data are interpreted in the light of Plasmodium falciparum malaria selection and population movements in the African subcontinent.

Africa, Southern↗
PubMed1991

Techniques used to define human MHC antigens: restriction fragment length polymorphisms.

Polymorphisms within the HLA-DRB1, -DRB3, -DQB1 and -DQ A1 genes are detectable using restriction fragment length polymorphism (RFLP) analysis. DNA is isolated from EDTA-treated blood or from spleen or lymph nodes. The DNA is digested to completion with the restriction endonuclease TaqI and resolved using agarose gel electrophoresis. The DNA after denaturation is then transferred to a nylon membrane (Southern blotting) and hybridised with radiolabelled cDNA probes: HLA-DR beta pRTV1, HLA-DQ beta pII-beta-1 and HLA-DQ alpha pDCH1. After autoradiography the membrane is dehybridised prior to rehybridisation. This system is very useful in those situations where serological assignment is difficult due to poor quality or low numbers of circulating B cells and where there is a lack of reliable antisera for certain specificities. The RFLP techniques can also define subtypes of DR and DQ serological specificities. However, certain alleles have the same RFLP. In some instances by identifying the DQ allele the DR allele can be determined by association due to linkage disequilibrium (e.g., DRw17-Dw25-DQw2 and DRw13-Dw25-DQw6). In other instances (e.g., DR1 and DRBr), the problem can be resolved using serology. In addition the RFLP system cannot be applied prospectively to the cadaver donor situation because of time restrictions. Thus the RFLP system complements existing serological techniques. However, it can be very useful as a quality control for the serological methods especially in the assessment of the quality of antisera and in the determination of discrepancies between centres.(ABSTRACT TRUNCATED AT 250 WORDS)

Alleles↗
PubMed1990

Restriction fragment length polymorphism of bovine lysozyme genes.

Genetic polymorphism of bovine lysozyme (LYZ) genes was investigated by analysing restriction fragment length polymorphism (RFLP). The analysis revealed three RFLP loci designated LYZ1, LYZ2 and LYZ2. Each system included two or three allelic variants. Evidence for close genetic linkage of the three loci was found. There was also a significant linkage disequilibrium among the three loci in a sample of about 200 breeding bulls from one breed. No statistically significant association was found between LYZ RFLPs and breeding values of bulls for disease or milk production traits.

Alleles↗
PubMed1989

Restriction fragment length polymorphisms mapped in spontaneously hypertensive rats using kallikrein probes.

We have explored the role of kallikrein-kinin system in essential hypertension using spontaneously hypertensive rats (SHR) as an animal model. A rat tissue kallikrein complementary (c) DNA (RSK 1105) was used as a probe in Southern blot hybridization to detect restriction fragment length polymorphisms (RFLPs) in SHR. Using 23 different restriction endonucleases, we have identified five RFLPs involving alterations in restriction fragment lengths for the restriction enzymes Bgl II, Dra I, Nde I, Sph I, and Bcl I. Three of the enzymes, Nde I, Sph I, and Bgl II, generate multiple polymorphic fragments. We have further mapped these RFLPs with two additional probes, both from the rat renal kallikrein gene RSKG 7. The 5' probe, consisting of sequences approximately 2000 base pair (bp) 5' of the first exon, recognizes RFLPs in DNA digested with Bcl I and Sph I. The 3' probe, approximately 4400 bp away from the fifth exon, recognizes polymorphic fragments in DNA digested with Bcl I, Dra I and Nde I. These findings indicate possible differences in tissue kallikrein genes or their regulatory regions in SHR that could contribute to the pathogenesis of hypertension in this animal model.

Animals↗
PubMed1990

Detection of DNA polymorphisms between two inbred mouse strains--limitations of restriction fragment length polymorphisms (RFLPs).

Type I (insulin-dependent) diabetes in humans is characterized by a T cell mediated destruction of insulin-secreting pancreatic beta cells. This autoimmune response is very similar to that seen in the non-obese diabetic (NOD) mouse strain. Originally bred from the ICR cataract-prone strain, NOD mice spontaneously develop T cell mediated insulitis and type I diabetes by the age of 6 months. Backcross studies with the NOD mouse strain indicate segregation of at least three recessive genes. One of these, Iddm-1, has been shown to be tightly linked to the mouse MHC, H-2 on chromosome 17. Comparative studies with diabetic patients has also shown linkage to human HLA with protective and predisposing haplotypes being present within the population. In this study we have attempted to identify restriction fragment length polymorphisms (RFLPs) between the genomes of the NOD mouse strain and the diabetes-resistant strain C57BL/10. Such polymorphic loci will be used to screen DNAs from backcross animals that are diagnosed diabetic in an attempt to identify probes linked to the non-H2 disease susceptibility genes.

Animals↗
PubMed2004

[Molecular epidemiological analysis by IS1245-based restriction fragment length polymorphism typing on cases with pulmonary Mycobacterium avium disease observed in the same family].

INTRODUCTION: Mycobacterium avium-intracellulare complex (MAC) has become one of major human pathogens, however, its routes of transmission and environmental reservoirs causing human infection were not yet elucidated. We reported three families affected by pulmonary Mycobacterium avium (M. avium) disease. Previous reports on MAC diseases observed in the same family were very rare. The purposes of this study were to investigate whether the infected M. avium was the same strain among cases in the same family and to examine the possibility of human-to-human transmission, or infection from exposure to a common environmental reservoir. METHODS: M. avium isolates from nine cases of three families were examined by DNA polymorphism based typing technique, restriction fragment length polymorphism (RFLP) analysis using insertion sequence IS1245 as a probe, to type the strains. Some isolates were subcultured to a single clone. RESULTS: All strains isolated from cases in the same family showed different patterns by the RFLP analysis. And not only simultaneous polyclonal infection but also repeated polyclonal infections were observed in some patients. DISCUSSION: The results suggest importance of underlying anti-mycobacterial immunological impairment and defects of local defense rather than virulence of infected strains as the pathogenesis of pulmonary M. avium disease.

Aged↗
PubMed2002

Polymerase chain reaction based restriction fragment length polymorphism for the genotyping of cytomegalovirus (CMV) from patients with CMV disease in Chennai.

BACKGROUND & OBJECTIVES: Since cytomegalovirus (CMV) is heterogenous and exhibits genomic polymorphism, polymerase chain reaction (PCR)-based restriction fragment length polymorphism (RFLP) was applied to identify the glycoprotein B subtypes in patients diagnosed to have CMV disease. METHODS: CMV standard strain (AD 169) and 55 clinical specimens from 50 patients (35 males; 15 females) positive for CMV by PCR coding for the morphological transforming region II gene were subjected to PCR coding for gp 55 region of CMV gB gene. PCR amplified products were subjected to RFLP using Hinf I. RESULTS: Of 50 patients, 26 (52.0%) (20 males; 6 females) were positive by PCR (gB gene). Upon RFLP, AD 169 and CMV strains of 14 (53.8%) patients (14 males) were typed as subtype II, and 12 (46.1%) (6 males; 6 females) as subtype III. Of 11 paediatric patients, 7 (63.6%) were infected with CMV subtype II and 4 (36.4%) with subtype III. CMV strains of the dual specimens from 3 PCR positive patients belonged to the same subtype. INTERPRETATION & CONCLUSION: In this study on CMV genotypes, CMV gB subtypes II and III were found in 53.8 and 46.1 per cent patients studied respectively, while I and IV were not present.

Adult↗
PubMed1991

Identification of verotoxin type 2 variant B subunit genes in Escherichia coli by the polymerase chain reaction and restriction fragment length polymorphism analysis.

A set of synthetic oligonucleotide primers was designed for use in a polymerase chain reaction protocol to specifically detect the B subunit genes in vtx2ha and vtx2hb, which code for the production of the VT2 (Shiga-like toxin II) variant cytotoxins VT2v-a and VT2v-b, respectively. An additional set of primers amplified a fragment common to the B subunits of the VT2 and the VT2 variant genes. Subsequent restriction endonuclease digestion of this amplicon permitted prediction of specific VT2 and variant genotypes on the basis of predetermined restriction fragment length polymorphisms. Genotypes of 21 VT2-producing strains of Escherichia coli were determined using this polymerase chain reaction-restriction fragment length polymorphism procedure. Four strains contained B subunit target sequences only for VT2 genes, 9 strains contained sequences only for VT2v-a genes, and 3 strains contained sequences only for VT2v-b. For genes in combination, one strain contained B subunit genes for both VT2 and VT2v-a and two strains contained B subunit genes for VT2 and VT2v-b. Two strains of E. coli O91:H21 contained both VT2v-a and VT2v-b B subunit genes. The VT2 reference strain of E. coli, E32511, was found to contain the targeted sequences from both VT2 and VT2v-a genes, whereas the recombinant E. coli, pEB1, possessed only that of the VT2 gene. The specific activities of extracellular VT2 determined in HeLa cells ranged from 0.3 to 41.7 TCD50 per microgram of protein in strains carrying the VT2 gene target and from 0 to 50.0 TCD50 per microgram of protein in strains carrying only the VT2 variant target (TCD50 is the tissue culture dose by which 50% of the cells were affected), suggesting that phenotypic expression does not correlate with genotype.

Animals↗
PubMed1993

Polymerase chain reaction-based restriction fragment length polymorphism analysis of a fragment of the ribosomal operon from Rochalimaea species for subtyping.

Restriction endonuclease analysis of a polymerase chain reaction-amplified DNA fragment which included the spacer region between the genes coding for 16S and 23S rRNAs and a portion of the gene coding for 23S rRNA (spacer + 23S) was done on 10 previously characterized clinical isolates of Rochalimaea henselae, one clinical isolate of Rochalimaea quintana, and the type strains of R. henselae, R. quintana, Rochalimaea vinsonii, and Bartonella bacilliformis. Brucella abortus DNA was not amplified by the primer set used. The clinical isolates of Rochalimaea were obtained from blood or tissue from patients with and without preexisting disease. The amplicon from each strain was digested with five endonucleases (AluI, HaeIII, TaqI, HinfI, and MseI). AluI and HaeIII were useful in species differentiation and subtyping of R. henselae. R. henselae isolates showed six different restriction patterns with AluI and four patterns with HaeIII. TaqI, HinfI, and MseI were useful only in species differentiation. These observations indicate that PCR amplification of the spacer + 23S region of the ribosomal DNA of Rochalimaea spp., along with restriction endonuclease analysis, allows differentiation of Rochalimaea spp. from closely related genera, differentiation among the species within Rochalimaea, and differentiation of strains within R. henselae. The subtyping potential of this method may be useful for further clinical and epidemiologic studies of the spectrum of diseases caused by R. henselae.

Bacterial Typing Techniques↗
PubMed2001

recA genotyping of Salmonella enteritidis phage type 4 isolates by restriction fragment length polymorphism analysis.

AIMS: To subtype Salmonella enteritidis phage type 4 isolates by using recA genotyping. METHODS AND RESULTS: Random amplified polymorphic DNA analysis using a primer ERIC2 of 76 isolates of Salmonella enteritidis phage type 4 obtained in Northern Ireland in 1998 and in 1999 demonstrated the presence of five genotypes. Restriction fragment length polymorphism analysis, using a degenerate primer pair designed to amplify a segment (about 640 bp in length) of the recA gene from several members of the Enterobacteriaceae with restriction enzymes, HhaI and Sau3AI, showed that the resulting fragments could differentiate the isolates into three groups, respectively. CONCLUSION: recA gene amplification and HhaI and Sau3AI restriction digestion was demonstrated to increase the differentiating power between isolates of Salmonella enteritidis phage type 4 by combining the patterns of the random amplified polymorphic DNA analysis procedure using a primer ERIC2. SIGNIFICANCE AND IMPACT OF THE STUDY: A novel restriction fragment length polymorphism assay for isolates of Salmonella enteritidis phage type 4, based on the amplification of the recA gene was attained and its comparison and its combination with random amplified polymorphic DNA analysis was provided.

Bacterial Proteins↗