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Results for “Polymorphism, Restriction Fragment Length”

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PubMed1992

High levels of linkage disequilibria between serologically defined class I bovine lymphocyte antigens (BoLA-A) and class II DQB restriction fragment length polymorphism (RFLP) in Norwegian cows.

Serum defined BoLA-A antigens, together with BoLA-DQB RFLP patterns, were determined in 87 almost unrelated Norwegian cattle. Statistical analysis revealed strong linkage disequilibria between these loci at the population level. A total of 13 haplotypes were found to be present at frequencies significantly greater than those predicted on the basis of their component gene frequencies. Among these, the subgroups 1A and 1B of the DQ1 haplotype were found to be closely associated with the class I antigens A11 and w16, respectively. The association between A11 and DQ1A is of particular interest, as two independent studies, one employing class I serology, and the other RFLP analysis of the class II locus DQ, have previously indicated that A11 and DQ1A confer relative susceptibility to mastitis.

Alleles↗

PubMed1997

Study of the alcohol dehydrogenase-1 (Adh1) gene in tetraploid corn: expression in the pollen grains and restriction fragment length polymorphism.

The results of two separate experiment are presented in this paper. In the first experiment pollen assays were carried out in Wf9 tetraploid maize plants in order to decide whether the lack of the ADH enzyme activity in the pollen grains was caused by a 'O' allele or an active transposon. On the basis of the results we suppose that the reduced ADH enzyme activity in the pollen grains is the result of a transposon affecting only the gametophyte. In the second experiment a maize Adh1-S genomic clone was constructed by polymerase chain reaction (PCR) and used as a probe to detect polymoprhism around the Adh1 gene in W117 S18 tetraploid maize sublines. The PCR20-EcoRI clone-enzyme combination resulted in a monomorphic RFLP pattern. The PCR20-Bgl II probe-enzyme combination yielded a multiple-banded pattern.

Alcohol Dehydrogenase↗

PubMed1999

Simultaneous infection with two strains of Mycobacterium tuberculosis identified by restriction fragment length polymorphism analysis.

Simultaneous infection with two different strains of Mycobacterium tuberculosis has been demonstrated using phage typing. We report here the first case of mixed infection identified using IS6110-based genotyping of M. tuberculosis. The patient was diagnosed with pulmonary tuberculosis in February, 1991. The initial isolate of M. tuberculosis had two different genotype patterns (dark 7-band and light 14-band patterns). However, in a repeat isolate obtained several months later, only the 14-band pattern was visible. Exogenous reinfection and laboratory cross-contamination were unlikely because both genotype patterns were unique in the San Francisco database which includes over 1300 isolates of M. tuberculosis. This case demonstrates the importance of identifying mixed infections in the study of the molecular epidemiology of tuberculosis. Mixed infections could be confused with exogenous reinfection or laboratory cross-contamination, and important epidemiologic connections could be missed.

Antitubercular Agents↗

PubMed2001

Identification of Biomphalaria havanensis and Biomphalaria obstructa populations from Cuba using polymerase chain reaction and restriction fragment length polymorphism of the ribosomal RNA intergenic spacer.

In Cuba, several Biomphalaria species have been reported such as B. orbignyi, B. schrammi, B. helophila, B. havanensis and B. peregrina; only the latter three are considered as potential hosts of Schistosoma mansoni. The specific identification of Biomphalaria species is based on anatomical and morphological characters of genital organs and shells. The correct identification of these snails is complicated by the high variation in these characters, similarity among species and in some cases by the small size of the snails. In this paper, we reported the classical morphological identification, the use of PCR and RFLP analysis of the internal transcribed spacer region of the ribosomal RNA genes for molecular identification of seven snail populations from different localities in Cuba. Using morphological and molecular analysis, we showed that among the studied Cuban Biomphalaria populations only B. havanensis and B. obstructa species were found.

Animals↗

PubMed1999

Relation of the bi-allelic NcoI restriction fragment length polymorphism within the tumour necrosis factor B gene to the development of mediastinitis.

During recent years the dual role of endogenous inflammatory mediators such as tumour necrosis factor (TNF) has become evident. While TNF has been recognised to possess a great detrimental potential, for example in the case of sepsis, it is on the other hand an integral component of an adequate immune response to bacterial invasion. These different properties of TNF and others seem to be dependent mainly on the quantitative extent of their formation. Some recent findings indicate that this extent may in part be determined genetically. The classification of patients according to polymorphic cytokine genes might, therefore, predict some of their reactions to septic challenges.

Alleles↗

PubMedDate not supplied

Restriction fragment length polymorphisms, glucocorticoid receptors, and phenytoin-induced cleft palate in congenic strains of mice with steroid susceptibility differences.

A gene that affects susceptibility to cortisone-induced cleft palate maps between H-2S and H-2D on mouse chromosome 17. Congenic mouse strains that differ at this locus, designated Cps-1 (cleft palate susceptibility-1), have been tested for the presence of several closely linked markers. All data obtained so far are consistent with a gene order of H-2S-Cps-1-BAT-5-BAT-2-TNF-H-2D. The Cps-1 gene does not appear to affect the level of glucocorticoid receptors or the susceptibility of mice to phenytoin-induced cleft palate.

Animals↗

PubMed1985

Analysis of three restriction fragment length polymorphisms in the human type II procollagen gene.

Cloned genomic DNA sequences corresponding to various regions of the human type II procollagen gene were used to analyze the DNA from 78 normal volunteers. Southern hybridization experiments detected polymorphic HindIII, BamHI, and EcoRI sites. The presence of the polymorphic HindIII site results in a 7.0-kilobase (kb) band, and the absence of this site results in a 14.0-kb band. When present, the BamH1 polymorphic site yields a 4.8-kb band, and when absent, yields a 7.2-kb band. The presence of the EcoRI polymorphic site results in a 3.7-kb band, and its absence results in a 7.0-kb band. Each polymorphic site was mapped. Analyses of the data demonstrated that the sites are present in overall gene frequencies of .39 for HindIII, .04 for BamHI, and .02 for EcoRI. Gene frequencies of the polymorphic sites were also studied with respect to race. The polymorphic sites are present in a Hardy-Weinberg distribution in the study population. Study of an extended family demonstrated that the segregation of the HindIII polymorphic site is consistent with Mendelian inheritance.

Deoxyribonuclease BamHI↗

PubMed1996

Restriction fragment length polymorphism (RFLP) analysis on DNA from human compact bone.

DNA typing techniques primarily identify specific genetic markers that are highly polymorphic within a population and have found great utility in forensic science. The established DNA identification protocol, termed restriction fragment length polymorphism (RFLP), has been admitted as physical evidence in the investigation of crimes such as assault, sexual assault, and homicide. The limitation associated with this procedure concerns the integrity of the genetic material. This study sought to evaluate human bone as a source material for DNA identification following exposure to common forensic field conditions. Often, with the onset of decomposition and eventual disarticulation of a body, soft tissues, hair and teeth may not be recovered. The significance of this study lies in the fact that, within forensic anthropology, human bone represents the most biologically stable evidence and is sometimes all that remains after periods of exposure. Genomic DNA was extracted from human bone following exposure to surface deposit, shallow burial, and fresh water immersion. Samples were collected over a three month time course and analyzed by spectrophotometry and agarose gel electrophoresis as well as RFLP analysis. The data suggest that high molecular weight DNA may indeed be extracted from human bone and typed by RFLP analysis for use in forensic identification. Under simulated forensic field conditions, the severity of DNA degradation was in the order of fresh water immersion > shallow burial > surface deposit. Genomic DNA from bone deposited on the desert surface for up to 4 weeks was detected by RFLP analysis. No spurious bands were detected in any specimens, and to the extent that bands were still present, the RFLP patterns matched. These findings demonstrate that human bone can be a reliable source of genomic DNA, and that bone recovered from surface deposit is the most desirable for use in forensic identification.

Bone and Bones↗

PubMed1995

A CYP1A1 restriction fragment length polymorphism is associated with breast cancer in African-American women.

We examined the role of CYP1A1 polymorphisms as potential molecular markers of breast cancer susceptibility in Caucasian and African-American women. The case-control study involved 51 women with breast cancer and 269 female controls. In African-Americans, the frequency of the homozygous MspI polymorphism was 3.5% in controls and 19% in breast cancer cases. The odds ratio of breast cancer with the MspI homozygous variant was 9.7 (95% confidence interval: 2.0-47.9). This association was not observed in Caucasian women. The exon 7 and AA polymorphisms were not associated with breast cancer in either group. The mechanism for the observed association between the MspI polymorphism and breast cancer is unclear. It is possible that the CYP1A1 MspI RFLP is linked with other polymorphisms in the African-American population, either in the CYP1A1 gene, which is involved in estrogen metabolism, or other genes related to risk of breast cancer.

Adult↗

PubMed2005

Restriction fragment length polymorphism of exon 2 Ovar-DRB1 gene in Polish Heath Sheep and Polish Lowland Sheep.

Exon 2 of the Ovar-DR gene is known to encode the MHC outer domain (alpha or beta chain) that forms the binding area to antigens presented. The study was aimed at analysing exon 2 Ovar -DRB1 gene polymorphism in Polish Heath Sheep and Polish Lowland Sheep (Zelazna variety). A total of 101 and 99 ewes of the respective breeds were included in this study. We identified 65 different haplotypes in Polish Heath Sheep and 68 in Polish Lowland Sheep. The PCR-RFLP method and PCR products sequencing made it possible to identify two new sequences of exon 2 Ovar-DRB1 gene (AY230000 and AY248695). A distinct polymorphism in the exon 2 sequence presents possibilities for immune response toward a great variety of pathogens.

Animals↗

PubMed2005

Novel PCR-restriction fragment length polymorphism method for determining serotypes or serogroups of Streptococcus pneumoniae isolates.

Serotyping Streptococcus pneumoniae is a technique generally confined to reference laboratories, as purchasing pneumococcal antisera is a huge investment. Many attempts have been made to modify serological agglutination techniques to make them more accessible, and more recently developments in serotyping have focused on molecular techniques. This paper describes a PCR assay which amplifies the entire capsulation locus between dexB and aliA. Amplicons are digested to produce serotype-specific patterns. We have shown, using 81 epidemiologically unrelated strains representing 46 different serotypes, that the patterns correlate with a 90 to 100% similarity range for the same serotype or serogroup. Prospective testing of 73 isolates of unknown serotype confirmed reliable serotype attribution, and serotype profiles are reproducible on repeated testing. Once our database contains all 90 serotypes, this technique should be fully portable, cost-effective, and useful in any laboratory with sufficient molecular experience.

Bacterial Typing Techniques↗

PubMed1989

Analysis of restriction fragment length polymorphism in lymphokine genes of normal and autoimmune mice.

Analysis of RFLP has been employed in lymphokine genes of autoimmune and normal mice. No polymorphism could be detected in the loci containing IL-2, IL-2 receptor, IL-5, and IFN-gamma in NZB, NZW, BxSB, and MRL/lpr mice when compared with normal mice. Allelic forms were identified in the IL-1 alpha gene of BALB/c and in the IL-4 gene of NZW. The frequency of the Bam HI RFLP in the TNF-alpha gene of NZW which has been proposed to be associated with the development of autoimmune disease in (NZB x NZW)F1 mice has been analyzed in a number of different inbred strains and in wild mice. Since the same allele is inherited in most autoimmune, healthy laboratory and wild mice the TNF-alpha gene does not seem to be one of the causal agents that contributes to the development of autoimmunity in (NZB x NZW)F1 mice.

Animals↗

PubMed2001

Mycobacterium bovis: polymerase chain reaction identification in bovine lymphonode biopsies and genotyping in isolates from Southeast Brazil by spolygotyping and restriction fragment length polymorphism.

Diagnosis of the Mycobacterium tuberculosis complex by direct PCR of mediastinal lymphnode DNA and microbiological tests were compared in cattle suspicious of bearing tuberculous-like lesions detected during slaughter. The PCR procedure applied on DNA samples (n=54) obtained by adding alpha -casein into the thiocyanate extraction mix was positive in 70% of the samples. PCR confirmed the identification of 23 samples (100%) that grew in culture, 9 samples (60%) that failed to grow in culture, plus 6 (37.5%) samples that resulted in growth of bacterial contaminants. Genotyping by IS6110-RFLP and DR-spoligotyping analysis of seven samples revealed the presence of several polimorphisms. Seven of the isolates contained multiple copies of IS6110, thus defining the existence of five singular genotypes.

Animals↗

PubMed1989

Restriction fragment length polymorphism analysis of hematopoietic cells following successful treatment of relapsed acute lymphoblastic leukemia following bone marrow transplantation.

Despite aggressive therapy for leukemia in the form of bone marrow transplantation (BMT) relapse occurs in a significant number of cases. The origin of the leukemic relapse, whether it is of donor or recipient origin, and how best to treat the patients continue to pose problems for the clinician. In this paper we present a case in which the cytogenetics suggested that the relapse was of donor origin; however, molecular analysis revealed that the leukemic population was of host origin. The leukemic relapse following the BMT was treated with a second BMT. This resulted in a remission of 28 months after which leukemic relapse was again diagnosed. Using conventional chemotherapy it was possible to obtain another complete remission. This case illustrates a pitfall to cytogenetic analysis and two contrasting methods of dealing with leukemic relapse following BMT.

Adult↗

PubMed1993

[The association of HincII/low density lipoprotein receptor (LDLR) restriction fragment length polymorphism (RFLP) with diabetes mellitus and its lipid phenotype with PCR gene amplification].

The association of low density lipoprotein receptor (LDLR) gene HincII RFLP with diabetes mellitus and its lipid metabolism was studied in 196 Chinese with PCR gene amplification. 16 IDDM and 75 NIDDM were included. The most common genotype and allele frequencies of NIDDM were H2H2 (0.78) and H2 (0.89) respectively, and no significant differences were found in comparison with the normal control. The NIDDM with low LDL level (< 1.3 mmol/L) had less H2H2 type and H2 frequencies. Allele 1 (H1) was possibly related to the higher level of serum cholesterol, but allele 2 (H2) was quite the reverse. The phenotype of lipid metabolism was partially determined by the genotype. LDL, tc and tg level of NIDDM were significantly higher than the normal control (P < 0.001, 0.001, 0.05 respectively), indicating that NIDDM was accompanied by disturbance of lipid metabolism.

Adolescent↗

PubMed1987

Use of cyanuric chloride-activated paper for detection of subpicogram quantities of specific DNA sequences and its application to linked restriction fragment length polymorphism analysis in a Duchenne muscular dystrophy affected family.

Conditions for the optimal use of cyanuric chloride-activated (CCA) paper in Southern transfer hybridization experiments of genomic DNA were investigated. They depend critically on pH and ionic strength during transfer and on the composition of the hybridization solution. Simplified hybridization conditions using a SSC/dextran sulfate system at 65 degrees C without sodium dodecyl sulfate and the complex Denhardt's solution are applied. CCA paper allows repeated use in hybridization experiments. Under optimized conditions CCA paper allows a more sensitive detection of single-copy gene sequences in the subpicogram range than do nylon membranes. Application of these transfer and hybridization conditions with our newly developed CCA paper to carrier determination and prediction of the healthy male haplotype demonstrates its usefulness for prenatal counseling of a Duchenne muscular dystrophy family.

DNA↗

PubMed1996

A novel Tth111I restriction fragment length polymorphism (RFLP) allows tracing of X-chromosome inactivation in the (Xid) heterozygote.

The X-linked immunodeficiency (Xid) in CBA/N mice serves as a model for the X-linked agammaglobulinemia (XLA) syndrome in man. X-chromosome inactivation in F1 heterozygotes derived from CBA/N (Xxid/Xxid) and B6.Pgk-1a (X+/Y) was investigated by monitoring the methylation status of the individual Pgk-1 alleles, Pgk-1b and Pgk-1a, respectively, using a novel Tth111I RFLP. Results indicate that in circulating B lymphocytes of female heterozygotes, only the X chromosomes carrying the normal alleles (X+) are active (nonrandom inactivation of the X chromosome), whereas in non-B cells both the X chromosomes (X+ and Xxid) are active (random inactivation of the X chromosome). These results were further confirmed by direct evaluation of transcription of the Btk gene, the gene mutated both in Xid and in XLA.

Agammaglobulinaemia Tyrosine Kinase↗

PubMed1991

Restriction fragment length polymorphisms associated with the factor VIII and factor IX genes in Polynesians.

New Zealand Maoris (72 X chromosomes) have been compared with Pacific Island Polynesians (121 X chromosomes) and Caucasian New Zealanders (51 X chromosomes) as a control group to determine the allelic frequency of six RFLPs associated with the genes for two X linked diseases (haemophilia A and haemophilia B). RFLPs examined were BclI, XbaI, and BglI within the factor VIII gene, the factor VIII extragenic TaqI system, and the factor IX intragenic TaqI and XmnI sites. The information obtained facilitates the design of strategies for both carrier detection and prenatal diagnosis of haemophilia A within these groups. Strong linkage disequilibrium was observed between the factor VIII BclI and XbaI sites in Polynesians. Genetic counselling for Polynesians with haemophilia B continues, however, to rely on phenotypic diagnosis. The RFLP data from the two separate loci on the X chromosome in Polynesians show similarities with Chinese and Japanese populations, reinforcing theories of an early Polynesian ancestry originating in east Asia.

Alleles↗