PubMed Health⌕ Search

SEARCH · PubMed Health

Results for “Polymorphism, Restriction Fragment Length”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 973 records · Page 54Linked to original sources
PubMed1995

High-resolution HLA-DQB1 typing by combination of group-specific amplification and restriction fragment length polymorphism.

A reliable method for high-resolution HLA-DQB1 typing using the combination of group-specific amplification and RFLP analysis is described. Group-specific amplification was carried out for the alleles of two groups using the two primer pairs under the same PCR conditions. One group contains DQ5 and DQ6 specificities and the other DQ2, DQ3, and DQ4 specificities. Computer analysis on cleavage patterns for 19 alleles of the DQB1 gene showed that the 11 alleles of the former group could be distinguished with five restriction enzymes and the eight alleles of the latter group could be distinguished with four enzymes. We could reduce the number of restriction endonucleases required compared with the number used in previous studies because we selected appropriate restriction enzymes which had at least one recognition site in almost all DQB1 alleles as a form of internal control. Moreover, DQB1*0602 and 0603, which were indistinguishable using the previously reported PCR-RFLP methods, could be distinguished by the present method. The results of typing of 100 samples from Japanese individuals by this method showed no discrepancy with the results obtained by serologic methods. The calculated allele frequencies showed good agreement with those reported at the 11th International Histocompatibility Workshop.

Base Sequence↗
PubMed1988

Restriction-fragment-length-polymorphisms close to the human insulin gene on chromosome 11 and their possible relation to diabetes mellitus in a GDR population.

A polymorphic DNA sequence flanking the 5'-region of the human insulin gene was studied by means of Southern blot hybridization techniques in 92 diabetic and non-diabetic individuals in order to investigate the possible relation of their allelic variants to certain types of diabetes. DNA was isolated from nucleated blood cells and digested with the restriction endonucleases EcoRI or Bg1 I. Only two classes of alleles were found (U and L). The small L-allele was predominantly found with the following frequency: 0.64 in controls, 0.795 in insulin-dependent diabetics, and 0.625 in non-dependent patients. It could be demonstrated that the L-allele and IDDM are associated. These data suggest that this allele seems to be a genetic marker for insulin-dependent diabetes mellitus. The putative function of the polymorphic region in the aetiology of diabetes mellitus and the possible genes being in linkage disequilibrium with it are not known so far.

Adult↗
PubMed1991

Fc gamma RII restriction fragment length polymorphism (RFLP): analysis in systemic lupus erythematosus and scleroderma and evidence of an alpha gene duplication.

The characteristic finding of high levels of circulating immune complexes in patients with the autoimmune connective tissue diseases systemic lupus erythematosus (SLE) or scleroderma has raised the possibility that these patients may have a primary defect in immune complex clearance. The Fc receptor for IgG (Fc gamma R) plays a central role in the phagocytosis of antibody complexes. We have analysed Fc gamma R (type II) RFLPs identified in TaqI- and MspI-restricted genomic DNA and found that their distribution in SLE and scleroderma did not differ significantly from controls. Hybridization with specific regions of the Fc gamma RII cDNA clone indicate that part of the Fc gamma RII alpha locus is duplicated in some individuals. A further Fc gamma RII gene has recently been identified (Fc gamma RII alpha'). This gene shows greater than 95% homology with Fc gamma RII alpha and may thus be the candidate gene for the apparent alpha duplication seen in some individuals. It is possible that an individual may possess one, two, three or four TaqI Fc gamma RII alpha/alpha' alleles, correlating with incidence and numerical heterogeneity in Fc gamma RII alpha and alpha'. The physiological effects of this numerical heterogeneity remain to be investigated.

Antigens, Differentiation↗
PubMedDate not supplied

DNA typing: analysis of restriction fragment length polymorphisms.

Genetic Technologies Corporation Pty. Ltd. was the first Australian commercial laboratory to use DNA typing for the purpose of determining human identity. Genetic Technologies holds the patient for the use of this technique in Australia (Australian Patent Number 577277) for individual identity in any species. In the five years since its beginning Genetic Technologies has conducted over 1200 paternity and 70 criminal cases.

DNA↗
PubMed2005

Genotyping of Campylobacter jejuni strains from Danish broiler chickens by restriction fragment length polymorphism of the LPS gene cluster.

AIMS: To apply and evaluate LG (LPS genes) genotyping, which is a genotyping method based on a cluster of genes involved in the synthesis of surface lipopolysaccharides (LPS) in Campylobacter species, for typing of Campylobacter jejuni isolates obtained from Danish broiler chickens. Furthermore, the LG genotyping method was used to study the genetic stability of four C. jejuni strains after gastrointestinal passage through experimentally infected chickens. METHODS AND RESULTS: In the present study, the LG genotyping method was modified with respect to the restriction enzymes used. To validate the method, 63 Penner serotype reference strains and 107 C. jejuni chicken isolates, representing the most common Penner serotypes of C. jejuni in Danish poultry, were selected for typing. The method was successfully used for typing all isolates and the LG genotype profiles were reproducible. There were no changes in the LG genotype of the C. jejuni strains obtained after experimental passage through chickens. CONCLUSIONS: All C. jejuni strains obtained from broiler chickens were typeable by the LG genotyping method. Application of the RsaI restriction enzyme improved the method in terms of ease and consistency of analyses and increase of discriminatory power. SIGNIFICANCE AND IMPACT OF THE STUDY: The LG genotyping method is a valuable tool for typing C. jejuni isolates obtained from poultry. However, the association between Penner serotyping based on passive haemagglutination of heat-stable antigens and LG genotyping was low when applied to poultry isolates. This is in contrast to previous studies on isolates of human origin that reported a high correlation between results obtained by the two typing methods (Shi et al. 2002).

Animals↗
PubMed1997

Restriction fragment length polymorphism analysis and random amplified polymorphic DNA analysis of Campylobacter jejuni strains isolated from patients with Guillain-Barré syndrome.

Campylobacter jejuni serotype O19 strains associated with the Guillain-Barré syndrome (GBS) and other strains were examined by restriction fragment length polymorphism (RFLP) analysis of polymerase chain reaction products of the flaA genes and by random amplified polymorphic DNA (RAPD) analysis. RFLP analysis showed that regardless of LIO serotype, geographic origins, or association with GBS, the O19 isolates shared an identical digestion pattern by each of four restriction endonucleases, DdeI, MboI, MseI, and AluI. In contrast, among C. jejuni O1 or O2 strains, RFLP patterns were different even among strains of the same LIO serotype. The results of the RAPD analysis were consistent with the flaA RFLP data. These data indicate that all of the O19 strains that were tested were closely related to one another whether they were or were not associated with GBS.

Animals↗
PubMedDate not supplied

Restriction fragment length polymorphisms at the ornithine transcarbamylase locus in normal Chinese.

Ornithine transcarbamylase (OTC) (EC 2.1.3.3) is an hepatic mitochondrial enzyme involved in the detoxication of ammonia; it catalyzes the second step of the urea cycle, and is X-linked in human beings. Deficiency of OTC results in ammonia intoxication and, often, in early infant death, especially in males. This report describes the use of a nearly full-length cloned human cDNA for OTC for Southern blot analysis of genomic DNA. The pattern of MspI, TaqI, HindIII and EcoRI restriction endonuclease sites from 28 control individuals of Chinese backgrounds is reported. A Southern blot by Msp I reveals invariant bands of 19.5, 5.2 and 1.9 kb respectively, as well as one set of polymorphic bands 6.6/6.2 kb. By TaqI, invariant bands are 4.8, 2.7, 1.9, 1.7 and 1.4 kb respectively, while polymorphic bands are found at 4.1/3.9 kb. By HindIII, 3.2 kb is invariant but 4.0/2.9 kb polymorphic. By EcoR I, invariant bands are 9.0, 3.6, 3.4 and 1.45 kb respectively, but 2.5 kb is polymorphic. Combined with study of the alteration of restriction sites in the informative pedigrees, this information is expected to allow accurate heterozygote detection and prenatal diagnosis of OTC deficiency.

Asian People↗
PubMed2001

Prevalence of virulent Rhodococcus equi in soil from five R. equi-endemic horse-breeding farms and restriction fragment length polymorphisms of virulence plasmids in isolates from soil and infected foals in Texas.

Rhodococcus equi isolates (462) obtained from 64 soil samples collected on 5 R. equi-endemic horse-breeding farms and isolates from 100 infected foals in Texas were examined to determine the prevalence and genotypic diversity of virulence-associated plasmids. Isolates were tested for the presence of 15-17-kDa virulence-associated protein antigens (VapA) by immunoblotting and virulence-associated plasmids by PCR. Plasmid DNAs were isolated and analyzed by digestion with restriction endonucleases for estimation of size and comparison of polymorphisims. Rhodococcus equi were isolated from soil of all 5 farms; however, virulent R. equi were only isolated from 3 of the 5 farms and represented 18.8% (87 of 462) of total isolates. Of the 87 virulent soil isolates, 56 (64.5%) contained an 85-kb type I plasmid, 23 (26.4%) an 87-kb type I plasmid, 7 (8%) a newly defined 85-kb type III plasmid (Tx 43), and 1 (1.1%) a newly defined 85-kb type IV plasmid (Tx 47). Of the 100 isolates from infected foals, 96 were virulent. Of the 96 virulent isolates, 51 (53.1%) contained an 85-kb type I plasmid, 39 (40.6%) an 87-kb type I plasmid, 4 (4.2%) an 85-kb type III plasmid (Tx 43), and 2 (2.1%) an 85-kb type IV plasmid (Tx 47). There are at least 4 different R. equi virulence-associated plasmids in Texas, 2 of which have not previously been described. Based upon virulence plasmid typing, there is geographic diversity among isolates of R. equi from clinical and environmental samples on horse-breeding farms in Texas. There is not a strong correlation between the presence of virulent R. equi in farm soils and the R. equi disease status of those farms.

Actinomycetales Infections↗
PubMed1996

Genetic diversity among Frankia strains nodulating members of the family Casuarinaceae in Australia revealed by PCR and restriction fragment length polymorphism analysis with crushed root nodules.

DNA extracted directly from nodules was used to assess the genetic diversity of Frankia strains symbiotically associated with two species of the genus Casuarina and two of the genus Allocasuarina naturally occurring in northeastern Australia. DNA from field-collected nodules or extracted from reference cultures of Casuarina-infective Frankia strains was used as the template in PCRs with primers targeting two DNA regions, one in the ribosomal operon and the other in the nif operon. PCR products were then analyzed by using a set of restriction endonucleases. Five distinct genetic groups were recognized on the basis of these restriction patterns. These groups were consistently associated with the host species from which the nodules originated. All isolated reference strains had similar patterns and were assigned to group 1 along with six of the eight unisolated Frankia strains from Casuarina equisetifolia in Australia. Group 2 consisted of two unisolated Frankia strains from C. equisetifolia, whereas groups 3 to 5 comprised all unisolated strains from Casuarina cunninghamiana, Allocasuarina torulosa, and Allocasuarina littoralis, respectively. These results demonstrate that, contrary to the results of previous molecular studies of isolated strains, there is genetic diversity among Frankia strains that infect members of the family Casuarinacaeae. The apparent high homogeneity of Frankia strains in these previous studies probably relates to the single host species from which the strains were obtained and the origin of these strains from areas outside the natural geographic range of members of the family Casuarinaceae, where genetic diversity could be lower than in Australia.

Actinomycetales↗
PubMed1986

Chromosome assignment and restriction fragment length polymorphism analysis of the anonymous DNA probe B79a at 7q22 (HMG8 assignment D7S13).

The anonymous DNA fragment B79a, which had previously been located to chromosome 7cen-7q22, has been more accurately assigned to 7q22 by dosage analysis in a patient hemizygous for a deletion of that region. By examination of a panel of genomic DNAs from unrelated individuals, digested with a number of different restriction enzymes, we have identified two frequent RFLPs detected by B79a. This probe will be important in the analysis of cystic fibrosis which has been mapped to the region around 7q22.

Chromosome Mapping↗
PubMed2003

Factor V Leiden detection by polymerase chain reaction-restriction fragment length polymorphism with mutagenic primers in a multiplex reaction with Pro G20210A--a novel technique.

Factor V Leiden (FVL) R506Q and Prothrombin G20210A are clinically important genetic mutations associated with increased susceptibility to venous thrombosis. The objective of our study was to design a polymerase chain reaction/restriction fragment length polymorphism (PCR/RFLP) reaction that allows simultaneous detection of these two mutations. The reaction can be used in routine diagnostic settings. We have analysed 4504 alleles for each mutation with a mutagenic primer-based PCR system with a low failure rate. The system eliminates the false positive FVL G1691A results associated with other PCR/RFLP caused by rare confounding mutations adjacent to restriction endonuclease recognition sites. This multiplex PCR/RFLP reaction is rapid, robust and dependable.

3' Untranslated Regions↗
PubMed1995

Restriction fragment length polymorphism analysis of PCR-amplified 16S ribosomal DNA of human Capnocytophaga.

The confusion in the taxonomic status of the genus Capnocytophaga has made identification of strains and studies on the role of this genus in infectious diseases equivocal. In this study 33 strains of Capnocytophaga including reference strains and various clinical isolates, were studied using RFLP analysis of 16S ribosomal RNA genes. The 16S ribosomal RNA (rRNA) gene sequences from whole cell suspensions and isolated genomic DNA samples were amplified by the polymerase chain reaction (PCR) using eubacterial specific primers. PCR products were purified and characterized by single digestions with 12 restriction endonucleases. Five of these, BanI, CfoI, HaeIII, HphI and RsaII were found to discriminate reproducibly between strains, and restriction patterns (ribotypes) produced by these were analysed to clarify the classification of Capnocytophaga strains. Dendrograms inferring similarities were derived from these data by the UPGMA method. This analysis produced three major clusters of strains, each of which was associated with a previously proposed species type strain: C. gingivalis, C. sputigena and C. ochracea. The results support the division of Capnocytophaga into three species and demonstrate that, despite the heterogeneity of this genus, the modified ribotyping method provides a simple, rapid and reproducible way to identify Capnocytophaga strains.

Bacterial Typing Techniques↗
PubMed1989

Human IGHC locus restriction fragment length polymorphisms in IgG4 deficiency: evidence for a structural IGHC defect.

In man, IgG4 is the least abundant of the four IgG subclasses, and its serum levels vary considerably from one subject to another. Its deficiency has been thought to lead to recurrent infections; nevertheless, it is also commonly found in healthy individuals (1/400 in the Italian population). In 39 subjects with IgG4 serum levels less than 1 microgram/ml, we used 4 different probes (described in the accompanying study, Bottaro et al., Eur. J. Immunol. 1989. 19: 2151) to examine 13 loci within the IGHC region and analyzed the RFLP for 7 of them. No aberrant restriction patterns were identified in any of the subjects, showing the absence of major IGHC structural alterations. The allele frequency of some loci, however, was significantly different from that of a control group of 95 random subjects. This variation was shown to depend on a selective increase in the number of homozygotes for the associated alleles, that reached significant levels for the IGHGP, G2, PG2, PG4 and SG4 loci, but not for SG1 and A2T. The highest value was reached for alleles in the PG4 region, just 5' of SG4. These data indicate that a minor structural IGHC defect is probably the cause of a significant fraction of IgG4 deficiencies. Moreover, the different association levels of the PG4 and SG4 regions suggest that this defect is likely to lie in an upstream regulatory region rather than in the structural G4 gene.

Gene Frequency↗
PubMedDate not supplied

Species identification of Streptococcus porcinus by restriction fragment length polymorphism analysis of 16S ribosomal DNA.

Streptococcus porcinus reference strains and routine isolates belonging to Lancefield's serogroup E, P, U and V and to various serotypes of serogroup E were examined for their 16S ribosomal DNA fingerprint pattern. Oligonucleotide primers complementary to 16S rRNA genes were used to amplify gene fragments by polymerase chain reaction from genomic DNA. The amplified 1450 bp fragment was subsequently digested with the restriction enzyme BpiI resulting in two fragments with a size of approximately 1250 bp and 200 bp. All 45 S porcinus investigated in the present study could be identified on the basis of this characteristic 16S rDNA fingerprint pattern and clearly differentiated from 16 control strains of various species and serogroups of genus Streptococcus. The present results demonstrate the potential application of 16S rDNA analysis for identification of S porcinus, a species which might express various group- and type-specific antigens.

Animals↗