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Results for “Polymorphism, Restriction Fragment Length”

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PubMed1994

Restrictive fragment length polymorphisms of markers 3'HVR and 24-1 and their applications in gene diagnosis of adult polycystic disease in Chinese.

Adult polycystic kidney disease was diagnosed with pedigree analysis using polymorphic DNA markers linked to the disease gene in 5 families. The markers were thoroughly characterized in the population. We noted two important markers, 3'HVR and 24-1, which flank the disease gene PKD1 in normal Chinese. Southern hybridization was used, and numerous 3'HVR/PvuII polymorphic allelic bands varied from 1.4 kb to 8.0 kb with a positive skew distribution. They were divided into 11 groups with an interval of 0.6 kb and a heterozygosity rate of 0.86. Allele frequencies were observed. When the probe 24-1 was hybridized with genomic DNA digested by TaqI, two alleles, B1 and B2, were detected with frequencies of 0.76 and 0.24, respectively. B1 was 3.8 kb in size and B2 was composed of 2 bands, 1.5 kb and 1.3 kb. The polymorphism information content was found to be 0.297. Using these two markers for linkage analyses of 5 affected families, we confirmed the linkage between 3'HVR and the disease gene PKD1 and made presymptomatic diagnosis of the members at risk.

Alleles↗

PubMed1989

Restriction fragment length polymorphism of cardiac myosin heavy chain gene in rats and its strain distribution.

The distribution of an RFLP in EcoRI fragments of the cardiac myosin heavy chain gene among 29 strains of laboratory rats was examined. Southern blot hybridization of rat genomic DNAs with rat cardiac myosin heavy chain cDNA as a probe demonstrated an interstrain variation in one of eight EcoRI fragments. Of the 28 inbred strains examined, 10 had a fragment of 10 kbp, whereas 18 had a fragment of 7.5 kbp. The 15 samples of the remaining strain (Iar: WI outbred stock) had fragments of either 7.5 kbp or 10 and 7.5 kbp, indicating that this strain has maintained heterogeneity of these fragments.

Animals↗

PubMed2006

TRFMA: a web-based tool for terminal restriction fragment length polymorphism analysis based on molecular weight.

UNLABELLED: TRFMA provides a Web environment for analyzing T-RFLP results based on molecular weights of the fragments, rather than the numbers of nucleotides, to increase accuracy. The 16S rRNA data are saved as an XML file containing around 650 sequences (light version) and a MySQL database containing around 50 000 sequences (full version), which are connected to Web server via PHP5 and manipulated on an Internet browser. AVAILABILITY: TRFMA is freely available at http://myamagu.dent.kyushu-u.ac.jp/bioinformatics/trfma/index.html and can be downloaded from the same site.

Algorithms↗

PubMed1999

Restriction fragment length polymorphism analysis of the flaA gene of Campylobacter jejuni for subtyping human, animal and poultry isolates.

233 strains of Campylobacter jejuni were subtyped by PCR-RFLP analysis of the flagellin (flaA) gene by double digestion with EcoRI and PstI (EP flaA-profiling). The strains represented a variety of common Penner heat stable (HS) serotypes and comprised isolates of human, bovine, ovine, chicken and canine origin. FlaA amplicons were obtained directly from DNA in cell lysates of most strains. RFLP analysis showed considerable allelic variation and nine EP flaA-types were identified of which the most common were type 2 (32%), type 3 (20%), type 4 (12%) and type 6 (12%). Other flaA-profiles each represented less than 10% of strains. C. jejuni strains of each serotype generally had one or two specifically associated flaA-types although some were features of several serotypes. Strains with the same flaA-type were found in different hosts. EP flaA-profiles were reproducible, clear and simple to record, and laboratory protocols were rapid and low cost with high throughput capacity. The EP flaA-profiling scheme provided an excellent molecular subtyping method to supplement HS serotyping, and reference strains are recommended to facilitate its use in future epidemiological investigations.

Animals↗

PubMed1996

Restriction fragment length polymorphism of HLA-DR and HLA-DQ allotypes in four endogamous groups of western India.

HLA-DR and HLA-DQ allele frequencies in four populations (Brahmin, Maratha, Gujarati Hindu Patel, and Parsi) of Bombay, western India, were analyzed using TaqI RFLPs detected by the cDNA probes DRB, DQB, and DQA. Although the overall differences in the HLA-DR and HLA-DQ genotype frequencies among the populations were not statistically significant, several population-specific haplotypes were significant. Multivariate analyses using data on 2 loci (HLA-DR and HLA-DQ) produced a meaningful pattern of genetic affinity and differentiation that parallels the analysis made when frequency data on 23 loci (21 blood group and protein loci and 2 class II antigen loci) are used. The RST for class II loci was 0.006; the genetic differentiation increased to 0.01 when data on 23 polymorphic loci were analyzed. The genetic affinity analysis shows the isolated nature of the Parsi and close genetic affinity between the two local populations of Bombay. Although the RFLP technique has several limitations compared with newly defined PCR-based methods, our analysis shows that the RFLP technique is still a useful adjunct method for studying HLA polymorphisms for which only limited data from the populations of the Indian subcontinent are available.

Consanguinity↗

PubMed2000

Cytologically integrated physical restriction fragment length polymorphism maps for the barley genome based on translocation breakpoints.

We have developed a new technique for the physical mapping of barley chromosomes using microdissected translocation chromosomes for PCR with sequence-tagged site primers derived from >300 genetically mapped RFLP probes. The positions of 240 translocation breakpoints were integrated as physical landmarks into linkage maps of the seven barley chromosomes. This strategy proved to be highly efficient in relating physical to genetic distances. A very heterogeneous distribution of recombination rates was found along individual chromosomes. Recombination is mainly confined to a few relatively small areas spaced by large segments in which recombination is severely suppressed. The regions of highest recombination frequency (</=1 Mb/cM) correspond to only 4.9% of the total barley genome and harbor 47.3% of the 429 markers of the studied RFLP map. The results for barley correspond well with those obtained by deletion mapping in wheat. This indicates that chromosomal regions characterized by similar recombination frequencies and marker densities are highly conserved between the genomes of barley and wheat. The findings for barley support the conclusions drawn from deletion mapping in wheat that for all plant genomes, notwithstanding their size, the marker-rich regions are all of similar gene density and recombination activity and, therefore, should be equally accessible to map-based cloning.

Chromosome Mapping↗

PubMed1990

Investigation of factor VIII:C gene restriction fragment length polymorphisms and search for deletions in hemophiliac subjects in Algeria.

The frequency of alleles for intragenic (intron 17 and intron 25) and extragenic (DXS15 and DXS52) F8C RFLPs was investigated in the Algerian population. Altogether 287 X chromosomes (97 males and 95 females) were studied. The allele frequencies found with the two intragenic F8C RFLPs were not substantially different from those reported in a Mediterranean population. At the highly polymorphic extragenic DXS52 locus the distribution in Algeria differed from that found in France. A new allele (14 kb), called 1 DZ, was found in 3.1% of the chromosomes. Fifty-one families with hemophilia A were studied with the same probes (374 subjects). Of the females, 94% were informative for at least one intra- or extragenic RFLP. Two recombinations were found between DXS52 and F8C, of which one occurred between the DXS15, DXS52 block and F8C, indicating that the two anonymous loci are on the same side of the F8C gene. Only two obvious gene deletions were observed in 73 unrelated hemophiliacs: one encompassed exons 14-22 (about 4.3 kb of cDNA and 36 kb of genomic DNA); the other removed the last exon (exon 26, representing 2 kb of cDNA).

Algeria↗

PubMed1996

[Restriction fragment length polymorphism of human renin gene in essential hypertension].

Essential hypertension is a heterogenous multifactorial disease resulting from an interaction between genetic and environmental factors. Nature of genes responsible for the blood pressure regulation is not completely understood. Data from molecular biology studies with animals indicate that renin gene is involved in the pathogenesis of hypertension. Renin gene is one of the major candidate genes contributing to the pathogenesis of essential hypertension in humans. The aim of this study was the assessment of the association of RFLPs of human renin gene with essential hypertension in Polish population and search for the genetic marker of susceptibility to the disease. MspI, HindIII and EcoT141 RFLP in human renin gene locus were studied and polymorphic allele and genotype frequencies in the population of 74 hypertensive and 60 normotensive subjects were compared. MspI and HindIII RFLP analysis has not shown any statistically significant differences in allele and genotype frequencies between hypertensives and normotensives. These RFLPs do not seem to be in association with essential hypertension in studied population. EcoT141 RFLP analysis has not shown statistically significant differences in polymorphic alleles frequencies between examined groups. However, the observed difference between genotype E2O frequencies in hypertensives (0.31) and normotensives (0.12) was statistically significant (p < 0.045). A clinical importance of this finding is not known but genotype E2O seems to be a potential marker of susceptibility to essential hypertension. Further investigations in larger group of patients are required.

Gene Frequency↗

PubMed2005

[PCR-restriction fragment length polymorphism assay (PCR-RFLP) as an useful tool for detection of mutation in gyrA gene at 86-THR position associated with fluoroquinolone resistance in Campylobacter jejuni].

The aim of this study was to investigate the mutations in gyrA gene at Thr-86 position in fluoroquinolone resistant C. jejuni clinical isolates (2003-2005). The change of Thr to Ile at 86 position is associated with high-level resistance to fluoroquinolone in C. jejuni. Thirty five (58%) of 65 C. jejuni strains were found to be resistant to ciprofloxacin using E-test method. PCR-RFLP technique with the RsaI enzyme was used for the identification of mutation in gyrA gene. The primers spanning a part of the fluoroquinolone resistance determining region (QRDR) were designed based on the article of Alonso et al. and the gyrA sequence of C. jejuni (Gen Bank accession number LO4566). One of this primer had mismatch introduced at the second nucleotide from 3' end of the primer what gives an artificial RsaI cleavage site. All of the ciprofloxacin-resistant isolates contained a single)point mutation in the gyrA gene: the replacement of Thr 86 by Ile. The results showed that PCR-RFLP is a rapid and simple method for the detection of the high-level fluoroquinolone resistance in C. jejuni.

Base Sequence↗

PubMed2003

Distribution analysis of IS231-like sequences among Bacillus thuringiensis serovars inferred from restriction fragment length polymorphisms.

The distribution of IS231 has been analyzed in Bacillus thuringiensis serovars. A 723-bp HaeII conserved fragment from IS231M has been used as a probe against EcoRI-digested B. thuringiensis total DNA to yield serovar-specific hybridization profiles. The approach was useful at revealing the extent of distribution of IS231-like sequences between and within strains. Of the 88 B. thuringiensis strains tested, 70 showed hybridization banding patterns that comprised between one and 20 distinct bands. These 70 B. thuringiensis strains were grouped based on banding pattern similarities. Interestingly, intraserovar strains did not necessarily cluster together.

Bacillus thuringiensis↗

PubMed1997

Restriction fragment length polymorphism study of Mycobacterium tuberculosis in Thailand using IS6110 as probe.

SETTING: Three referral hospitals in central Thailand. OBJECTIVE: To determine the population structure of Mycobacterium tuberculosis isolated from the referral hospitals. DESIGN: Study of 211 isolates of the bacteria received from the hospitals in central Thailand by Southern hybridization, with IS6110 probe and other probes when indicated. RESULTS: In 43 isolates only one copy of IS6110 was observed. These could be further differentiated by DR- and PGRS-specific probes. Two large groups of isolates with similar hybridization patterns were identified. The Beijing family, comprising 80 isolates, was previously reported to be commonly found in China, Mongolia, Thailand and Korea. The Nonthaburi group, comprising 29 isolates, were local strains. The age, sex and HIV status of the patients did not significantly correlate with the chance of being infected by isolates of any particular hybridization pattern. However, clustered isolates were found more commonly among the members of both the Beijing family and the Nonthaburi group. CONCLUSION: Southern hybridization with IS6110 was found to be useful in studying the epidemiology of tuberculosis in Thailand. The existence of the Beijing family was confirmed. The unusually wide spread of the Beijing family in several countries in Asia merits further investigation.

Adult↗

PubMed1995

Simple protocols for typing forensic biological evidence: chemiluminescent detection for human DNA quantitation and restriction fragment length polymorphism (RFLP) analyses and manual typing of polymerase chain reaction (PCR) amplified polymorphisms.

Methods for identity testing are described that enable extraction of DNA from biological samples, determination of the quantity of human DNA, and genetic analyses of the materials using restriction fragment length polymorphism (RFLP) typing and/or amplified fragment length polymorphism (AMP-FLP) typing of PCR products. The salient features of the procedures are simplicity, manual typing, nonradioactive chemiluminescent assays or silver staining for detection, and low cost. Most application-oriented laboratories involved in forensic and/or paternity testing should be able to implement these procedures.

Base Sequence↗

PubMed1989

XbaI restriction fragment length polymorphism of apolipoprotein B in Swedish myocardial infarction patients.

Apolipoprotein B (apoB) is a major importance to the metabolism of lipoproteins, and there is also evidence which suggests that apoB plays a central role in atherogenesis. In order to study whether there is a link between one of the mutations of the apoB gene and premature coronary heart disease, the frequency of the XbaI RFLP for the apoB gene was analysed in 52 male myocardial infarction patients. These were compared with a control group matched for age and sex (n = 52), and a random population sample of middle-aged men (n = 106). Two alleles were identified by the presence (X2) or the absence (X1) of an XbaI cleavage site. A somewhat higher frequency of the X2 allele was seen among the patients, however there was no significant difference between patients and controls regarding the genotypes or allele frequencies. This observation does not confirm one earlier report where a higher frequency of the X1 allele was seen in myocardial infarction patients. Differences between the studied populations or epidemiological designs of the studies might explain the diverging results. Further studies are evidently needed to fully resolve the relation between the XbaI RFLP and risk of atherosclerotic disease or lipoprotein metabolism.

Adult↗

PubMed1991

Diversity among DRw13 DQw7 haplotypes as revealed by serology Dw typing and restriction fragment length polymorphism.

HLA-DRw13 is in linkage disequilibrium with DQw6; an unusual association, DRw13 DQw7, is found in 2% of our Caucasoid population. Investigation of genotyped individuals and of families by two allosera and by Dw typing revealed two subtypes: one recognized by homozygous typing cell HAG and by two allosera, the other subtype remained unreactive with both reagents. Analysis of DNA fragments with DNA probes indicated that the HAG-negative subset had DNA fragments in common with DRw6 while the HAG-positive subset shared DNA fragments with DR5. However, all DRw13 DQw7 cells are Dw24 as seen by hybridization with DRB probe.

Genetic Variation↗

PubMed1991

Restriction fragment length polymorphism (RFLP) analysis in wheat. II. Linkage maps of the RFLP sites in common wheat.

Sixty-six F2 plants from the cross, Triticum aestivum cv. Chinese Spring (abbrev. CS) x T. spelta var. duhamelianum (Spelta), exhibiting the greatest number of RFLPs among eight common wheats, were analyzed for their RFLP genotypes using genomic DNA clones of CS as probes. In total, 204 RFLP loci were identified and their linkage relationships established. By nulli-tetrasomic analyses, all linkage groups were assigned to one another of the 21 wheat chromosomes. In addition, the carrier chromosomes of 228 non-RFLP loci were identified. The linkage maps of these RFLP loci have a total size of 1800 cM and exceed those of the classical genes in both size and locus number. Twenty loci show distorted segregation, four of which are clustered on chromosome 4A and three on the 2D chromosome. The CS alleles on 4A exhibit preferential transmission, while those on 2D exhibit depressed transmission, compared with Spelta alleles. This suggests the influence of gametic factors in those regions. RFLP loci are much fewer in the D genome than in the A and B genomes, but the numbers of non-RFLP loci are nearly the same in these three genomes. This suggests that Spelta wheat originated from a hybridization between T. dicoccum (spelt emmer) and T. aestivum.

Alleles↗

PubMed1989

Rabbit major histocompatibility complex. III. Multiple class II DR beta genes and restriction fragment length polymorphism of the class II alpha and beta genes.

Several class II alpha and beta chain genes of the rabbit MHC have been cloned and classified into three distinct subregions, R-DP, R-DQ and R-DR, based on their homology to the corresponding HLA-DP, -DQ and -DR genes. The organization of the rabbit MHC class II genes has now been studied in greater detail by analysing genomic DNA of an inbred III/J strain and several other RLA-D homozygous rabbits, with DNA probes derived from cloned R-DR beta genes. Eight previously cloned R-DR beta genes were shown to be allelic forms of five R-DR beta loci. Genomic blot analyses of DNA from seven rabbits homozygous for different RLA haplotypes revealed that the germline contains a total of approximately seven class II beta genes, one DQ beta, one DP beta and five DR beta. Extensive allelic polymorphism was identified by RFLP analysis using DQ and DR probes; limited RFLP was observed with DP probes. RFLP analyses allowed us to distinguish two haplotypes which had not been previously distinguished by MLR. Such RFLP analyses will be useful for identifying MHC 'compatible' rabbits for various immunobiological studies, including transplantation.

Animals↗

PubMed1995

[Detection of the kappa-casein genotype in bulls using restriction fragment length polymorphisms].

Genetic analysis of RFLP was used for detection of genotype and allele frequencies of kappa-casein in Slovakian Spotted (60 bulls) and Slovakian Pinzgau (22 bulls) cattle breeds, according to the method of Medrano et al. (1990). DNA was prepared from the semen of animals. In the Slovakian Spotted breed the frequencies of alleles were as follows: kappa-CnA = 0.666, kappa-CnB = 0.333. The frequencies of kappa-Cn A/A, A/B and B/B genotypes were 45.00, 43.33 and 11.66, respectively. In the 22 tested Pinzgau bulls, the frequencies of the A and B alleles were 0.682 and 0.318, respectively. The percentual occurrence of genotypes was also determined: 54.54 (kappa-Cn A/A), 27.27 (kappa-Cn A/B) and 18.18 (kappa-Cn B/B). Comparing our own results with those of Mácha et al. (1968), who carried out the analysis of distribution of the kappa-casein genetic variants in the same cattle breeds by starch gel electrophoresis of the milk samples of 170 cows (Tab. I), the 16 p.c. decrease of the allele B in the Slovakian Spotted cattle, lasting about 30 years, is very remarkable. The occurrence of homozygous genotype BB decreased by 35 p.c. In addition, the homozygous genotype AA increased by about 18 p.c. and the occurrence of heterozygous genotype is also higher by nearly 17 p.c. In the same comparison of the Slovakian Pinzgau breed, no difference was estimated in the allele frequencies of kappa-Cn (Tab. I).(ABSTRACT TRUNCATED AT 250 WORDS)

Alleles↗

PubMed2003

IS6110 restriction fragment length polymorphism of Mycobacterium tuberculosis isolated from patients with pulmonary tuberculosis in Campinas, Brazil: evidence of intercontinental distribution of strains.

Tuberculosis (TB) is a major concern in developing countries. In Brazil, few genotyping studies have been conducted to verify the number of IS6110 copies present in local prevalent strains of Mycobacterium tuberculosis, the distribution and clustering of strains. IS6110 DNA fingerprinting was performed on a sample of M. tuberculosis isolates from patients with AFB smear-positive pulmonary TB, at a hospital in Brazil. The IS6110 profiles were analyzed and compared to a M. tuberculosis database of the Houston Tuberculosis Initiative, Houston, US. Seventy-six fingerprints were obtained from 98 patients. All M. tuberculosis strains had an IS6110 copy number between 5-21 allowing for differentiation of the isolates. Human immunodeficiency virus infection was confirmed in nearly half the patients of whom data was available. Fifty-eight strains had unique patterns, while 17 strains were grouped in 7 clusters (2 to 6 strains). When compared to the HTI database, 6 strains matched isolates from El Paso, Ciudad de Juarez, Houston, and New York. Recently acquired infections were documented in 19% of cases. The community transmission of infection is intense, since some clustered strains were recovered during the four-year study period. The intercontinental dissemination of M. tuberculosis strains is suspected by demonstration of identical fingerprints in a distant country.

Bacterial Typing Techniques↗