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PubMed1992

Insertion/deletion polymorphism and other restriction fragment length polymorphisms in the MCC gene.

The MCC gene is a candidate as a tumor suppressor gene for colorectal neoplasms. Further, MCC is tightly linked to the familial adenomatous polyposis (FAP) locus by linkage and physical analysis. Hence, restriction fragment length polymorphisms (RFLPs) of this gene might be very useful for presymptomatic diagnosis of individuals in families segregating mutant alleles of the APC gene. Here we report the identification of five polymorphic systems in MCC gene (both cDNA and genomic), one of which is an insertion/deletion polymorphism that is detectable by a polymerase chain reaction method. These five RFLP systems should be useful for linkage studies in FAP and for examining loss of heterozygosity at this locus in colonic polyps and tumors.

Adenomatous Polyposis Coli↗
PubMed1991

[DNA polymorphism in the Mongolian population. Restriction fragment length polymorphism analysis of mitochondrial DNA].

Restriction enzyme fragment patterns in the D loop and deletion-insertion polymorphism in the V noncoding region of human mitochondrial DNA (mt DNA) were analysed in Mongolian population using the polymerase chain reaction. Polymorphisms were detected and mt DNAs classified into 40 types using seven enzymes--AvaII, BamHI, CfrI131, KpnI, EcoRV, HaeIII RsaI and Asian specific deletion and insertion. The allele frequencies of the polymorphisms and gene diversity were determined. The data obtained for Mongolian population and the literature data were comparatively studied.

Alleles↗
PubMed1987

Restriction fragment length polymorphism of the human T cell receptor alpha gene. I. Two polymorphic restriction sites localized to different regions of the gene.

Previous studies have demonstrated restriction fragment length polymorphisms (RFLP) in the vicinity of the alpha and beta genes of the human T-cell receptor. In the course of experiments designed to discover additional polymorphic restriction sites, we found a new RFLP of the T-cell alpha gene recognized by the restriction enzyme Taq I. The site was localized to the interval between the most 3' joining (J) exon and the most 5' constant (C) region exon, about 7 kb distant from the previously described Bgl II polymorphic site which mapped to the vicinity of the 3' untranslated exon. With the use of these two polymorphic markers, four Ti-alpha alleles could be identified, allowing unambiguous assignment of all Ti-alpha genes in some families. These markers may be useful in identifying possible immune response genes or disease predisposition genes associated with the genes of the T-cell receptor for antigen.

Alleles↗
PubMed1991

Complexity of Pseudomonas aeruginosa infection in cystic fibrosis: combined results from esterase electrophoresis and rDNA restriction fragment length polymorphism analysis.

Esterase electrophoretic typing and restriction fragment length polymorphism of ribosomal DNA regions (ribotyping) were used to differentiate 102 Pseudomonas aeruginosa clinical isolates obtained from chronic lung infection in 23 patients with cystic fibrosis (CF) and two reference strains (including the type strain ATCC 10145). Twenty-five zymotypes were obtained with the former method and 16 ribotypes with the latter. Combination of the two typing systems led to the finding of 30 different types. Our data highlights the physiopathological complexity of P. aeruginosa infection in CF as, in six individual cases, several types were found among isolates from a given patient. On the other hand, two unique types were found in two and three patients respectively, raising the possibility of cross-infections.

Cystic Fibrosis↗
PubMed1988

Restriction fragment length polymorphisms and an HLA-DRw52-associated split.

The restriction fragment length polymorphism technique, employing seven restriction endonucleases, and a DR-specific repeated element probe were used to study a large panel of homozygous typing cells in order to delineate haplotypic differences within the HLA-DRw52 supertype. Most of the restriction endonucleases revealed the presence of two allelic restriction fragment length polymorphisms correlating with and splitting the HLA-DRw52 supertypic specificity. One designated A, correlated with the HLA-DRw52 typing in HLA-DR5, HLA-DR3, (non-A1, B8), and some HLA-DRw6 haplotypes. The other, designated a, correlated with the HLA-DRw52 typing in HLA-DR5, HLA-DRw8, HLA-DR3 (A1, B8), and the remaining HLA-DRw6 haplotypes. The general applicability of these findings was validated in 47 HLA-typed laboratory controls.

Alleles↗
PubMed1988

Restriction fragment length polymorphism linkage map for Arabidopsis thaliana.

We have constructed a restriction fragment length polymorphism linkage map for the nuclear genome of the flowering plant Arabidopsis thaliana. The map, containing 90 randomly distributed molecular markers, is physically very dense; greater than 50% of the genome is within 1.9 centimorgans, or approximately 270 kilobase pairs, of the mapped DNA fragments. The map was based on the meiotic segregation of markers in two different crosses. The restriction fragment length polymorphism linkage groups were integrated with the five classically mapped linkage groups by virtue of mapped mutations included in these crosses. Markers consist of both cloned Arabidopsis genes and random low-copy-number genomic DNA clones that are able to detect polymorphisms with the restriction enzymes EcoRI, Bgl II, and/or Xba I. These cloned markers can serve as starting points for chromosome walking, allowing for the isolation of Arabidopsis genes of known map location. The restriction fragment length polymorphism map also can associate clones of unknown gene function with mutant phenotypes, and vice versa.

Bacterial Proteins↗
PubMed1990

Identification of restriction fragment length polymorphisms in DNA from Mycobacterium paratuberculosis.

DNAs from 34 mycobactin-dependent isolates of Mycobacterium paratuberculosis and 1 isolate of M. paratuberculosis 18 were digested with four restriction endonucleases. Southern hybridization experiments were performed with a 32P-labeled oligonucleotide DNA probe derived from the sequence of IS900, an insertion sequence present in 15 to 20 copies per M. paratuberculosis chromosome. The probe hybridized with DNA from each of the mycobactin-dependent isolates, and restriction fragment length polymorphisms were detected among the isolates with each restriction endonuclease used. Restriction fragment length polymorphism analysis may permit identification of various strains of M. paratuberculosis, which has not been possible with other techniques.

Animals↗
PubMed1992

Distribution of polymorphic HLA-DR and -DQ alleles as determined by restriction fragment length polymorphism analysis in an Austrian population.

The restriction fragment length polymorphism (RFLP) of HLA-DR beta, -DQ alpha and -DQ beta genes was analyzed in 637 unrelated individuals from the Austrian population. The restriction enzyme was Taq I, and three exon-specific probes were applied. The gene frequencies, the Hardy-Weinberg equilibrium in DR beta and DQ loci, linkage disequilibria between the loci and haplotype frequencies are calculated. Rare associations between DR and DQ loci are described. Two RFLP patterns are demonstrated which were unique in the overall 1,000 individuals tested so far.

Alleles↗
PubMed1992

The frequency of alpha 2-adrenoceptor restriction fragment length polymorphisms in normotensive and hypertensive humans.

OBJECTIVE: To examine the frequency of distribution of allelic polymorphisms of the alpha 2-adrenoceptor gene in normotensive and hypertensive humans. DESIGN: The frequency of alpha 2-adrenoceptor genotypes was compared in the two groups using the chi 2-test. SETTING: The Midwest Hypertension Research Center Outpatient Clinic of Creighton University School of Medicine. STUDY PARTICIPANTS: History was taken from and physical examination performed on each of the 60 hypertensive and 47 normotensive adults. METHODS: DNA was extracted from leukocytes from each participants. Twenty restriction endonucleases were used and one restriction fragment length polymorphism (RFLP) was found using a 950-bp restriction fragment from the coding region of the human platelet alpha 2-adrenoceptor gene (ADRA2R) and Bsu36I restriction endonuclease. This probe and Bsu36I restriction endonuclease, in addition to another restriction endonuclease (Dra I), were then used in the study. RESULTS: Three genotype patterns were found. Homozygotes for the Bsu36I RFLP have either a unique 12-kb or a unique 5.8-kb band. Heterozygotes have both bands. The frequency of this alpha 2-adrenoceptor RFLP was calculated. In hypertensives the frequencies of the 12- and 5.8-kb alleles were 0.52 and 0.48, compared with 0.45 and 0.55, respectively, in normotensive, a difference that was not statistically significant. CONCLUSIONS: The frequency of the Bsu36I RFLP involving an alpha 2-adrenoceptor gene in hypertensives did not differ significantly from that in normotensives. A genetic linkage study is now under way to test for an association of the Bsu36I RFLP of the alpha 2-adrenoceptor gene with essential hypertension in families.

Adult↗
PubMedDate not supplied

Applications of restriction fragment length polymorphism.

The availability of a variety of restriction endonuclease enzymes that cleave deoxyribonucleic acid (DNA) at specific sites has made it possible to identify the presence of polymorphic regions in the isolated fragments. Such restriction fragment length polymorphism (RFLP) results owing to a variation in the number of tandem repeats (VNTR) of a short DNA segment. These VNTR sequences can uniquely specify an individual and, as such, are used in DNA fingerprinting and in paternity testing. Restriction fragment length polymorphism may be found close to a disease gene, and, as such, can be used as a genetic disease marker. Certain criteria need to be fulfilled, however, for RFLP to be useful as a genetic disease marker, such as its closeness to the disease gene. Materials and methodology for detecting RFLP are reviewed with the current emphasis on amplification procedures utilizing the polymerase chain reaction (PCR).

Genetic Diseases, Inborn↗
PubMed1992

Restriction fragment length polymorphism analysis of zoo animals using HaeIII and four single-locus probes.

Using HaeIII as the restriction endonuclease, restriction fragment length polymorphism analysis of dried blood samples from various animals was conducted. Single-locus probes D2S44, D10S28, D1S7, and D4S139, as well as monomorphic probe D7Z2, were used to examine for banding patterns. If bands were present, the samples were further examined for heterogeneity (whether single or multiple bands were observed) and polymorphism (whether variation in band location was shown between the animals studied within a species). Blood samples from animals, including primates, were obtained from Miami Metrozoo, Miami, Florida. Some of the animals were non-related individuals while others were related. Banding patterns were observed in colobus' for D2S44, D1S7, and D4S139; owl monkeys for D2S44; gorillas for D2S44 and D4S139; gibbons for D2S44 and D4S139; siamangs for D2S44, talapoins for DiS7; cranes for D1S7; and otters for D1S7. Based upon these, all of the animals for which a conclusion could be drawn appeared to be homozygous and monomorphic (exhibited only an invariant single band) for the loci examined except colobus' for D4S139, gorillas for D4S139, cranes for D1S7, and otters for D1S7.

Animals↗
PubMed1990

Hae III--a suitable restriction endonuclease for restriction fragment length polymorphism analysis of biological evidence samples.

Hae III has been selected by our laboratories as the restriction endonuclease of choice for restriction fragment length polymorphism analysis of forensic science samples. The enzyme is compatible with the D2S44 probe system and generates relatively small DNA fragments for that marker system. Similarly, Hae III is compatible with several other independent polymorphic loci, including D1S7, D4S139, D16S85, D17S74, D17S79, D14S13, and D20S15. Hae III is functional under a variety of adverse conditions for DNA digestion and is not affected by the methylation pattern in mammals. Finally, Hae III is a relatively inexpensive restriction endonuclease.

Base Sequence↗
PubMed1988

Carrier detection in severe (type III) von Willebrand disease using two intragenic restriction fragment length polymorphisms.

DNA from a family with a female member affected with severe (type III) vWD was analysed using three restriction enzymes and a partial vWF cDNA probe. Two restriction fragment length polymorphisms (RFLPs) detected with the enzymes Bgl II and Xba I proved to be informative in this family. A 36.0 Kb allele demonstrated with the enzyme Xba I was rare in the general population but very important in this family for segregation analysis of the alleles and their association with the putative defective chromosome. The propositus was homozygous for the 36.0 Kb Xba I polymorphic band and heterozygous for the Bgl II polymorphism. She was the only member of the family showing this allelic pattern. The linkage of the alleles could be determined because her mother was homozygous for the 9.0 Kb Bgl II polymorphism but heterozygous for the Xba I polymorphism. The segregation of the alleles could be traced to the proband's son and a niece. The genotypic analysis revealed that her niece could be considered as carrying a defective gene for severe vWD.

Alleles↗
PubMedDate not supplied

Restriction fragment length polymorphisms at the methylmalonyl CoA mutase locus in normal Chinese.

L-methylmalonyl-CoA mutase (MCM; E.C. 5,4,99,2) is the apoenzyme for catalyzing the isomerization of L-methylmalonyl-CoA to succinyl-CoA. Genetic deficiency of MCM leads to the accumulation of precursors and abnormal metabolites of L-methylmalonyl-CoA. This can be associated with fulminant metabolic acidosis, widespread secondary aberrations in systemic metabolic homeostasis, mental retardation, or even neonatal death. This disorder is termed methylmalonic acidemia (MMA). This report, describes the use of an authentic, full-length cloned human cDNA probe, MCM26, kindly provided by Dr. Fred Ledley, for Southern blot analysis of genomic DNA. The pattern of EcoRI, Sac I and Hind III restriction endonuclease sites is reported from 14 unrelated control individuals of Chinese background. A Southern blot by EcoRI to the MCM26b probe reveals invariant bands of 4.1, 3.8, and 2.2 kb respectively. By EcoRI to the MCM26c probe, 7.2 kb is invariant. By HindIII to the MCM26c probe, invariant bands are 4.8 and 2.7 kb respectively. By SacI to the MCMb probe, invariant bands are 17, 8.0, 6.0, 3.6 and 1.8 kb respectively, while the polymorphic band is at 5.6kb. When combined with more diverse samples and additional polymorphisms, this restriction fragment length polymorphism may be useful for genetic diagnostic and linkage studies of MCM in MMA.

Chromosome Mapping↗
PubMed1992

Analysis of rRNA restriction fragment length polymorphisms from Bacteroides spp. and Bacteroides fragilis isolates associated with diarrhea in humans and animals.

The Escherichia coli rRNA operon rrnB was used as a 32P-labeled hybridization probe in Southern blots of genomic DNAs from representative strains of the saccharolytic, gram-negative, obligate anaerobes of the genus Bacteroides. Control experiments with the B. fragilis type strain ATCC 25285 established that nearly identical rRNA fragment patterns were produced when either the E. coli rrnB gene probe or homologous rRNA isolated from B. fragilis was used as the probe. In addition, it was shown that a specific 16S or 23S rrnB gene probe also could be used to produce fragment patterns suitable for analysis. Thirty-one strains from 8 of the 10 recognized Bacteroides species were then examined. The resulting autoradiographs revealed specific fragment patterns for all but one (B. ovatus) of the species tested. Restriction fragment length polymorphisms were observed for many of the strains tested, but these differences did not hinder species classification. The five B. ovatus strains examined did not form a distinct group, and their rRNA fragment patterns displayed a marked heterogeneity. The same approach was applied to a unique set of enterotoxin-producing B. fragilis strains isolated from animals and humans with diarrhea. The results demonstrated that these strains were in fact B. fragilis and that they produce rRNA fragment patterns closely related to those of the type strain ATCC 25285. This set of strains did not appear to form a separate subgroup or genotype within the B. fragilis species, and there were no distinguishable restriction fragment length polymorphisms that could be used to specifically separate enterotoxin-producing strains from nonenterotoxigenic strains.

Animals↗
PubMed1986

Restriction fragment length polymorphism of the human C3 complement gene.

A cloned gene-specific probe for human complement (C3) was hybridized to DNA samples digested with various restriction endonucleases. The C3 probe detects one restriction fragment length polymorphism (RFLP) that occurs frequently in the French population when DNAs are digested with Sac I. The corresponding DNA alleles can be readily used in linkage analysis of loci on chromosome 19, and such a polymorphism can be followed through myotonic dystrophy families.

Chromosomes, Human, Pair 19↗