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Results for “Polymorphism, Restriction Fragment Length”

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PubMed1993

Association of restriction fragment length polymorphism in alcohol dehydrogenase 2 gene with alcohol induced liver damage.

OBJECTIVE: To investigate the role of genetically determined differences in the enzymes of alcohol metabolism in susceptibility to liver damage from misusing alcohol. DESIGN: Use of pADH36 probe to study PVU II restriction length fragment polymorphism in alcohol dehydrogenase 2 gene in white alcohol misusers and controls. SETTING: Teaching hospital referral centres for liver disease and alcohol misuse. SUBJECTS: 45 white alcohol misusers (38 with alcoholic liver disease) and 23 healthy controls. MAIN OUTCOME MEASURES: Alcohol misuse, the presence and severity of alcoholic liver disease, alcohol dependency, and family history of alcohol misuse. RESULTS: A two allele polymorphism (A and B) was identified. In control subjects the allele frequencies were 85% for A and 15% for B compared with 37% and 63% respectively in alcohol misusers (p < 0.001). B allele was significantly associated with severe liver damage (p < 0.05) as well as alcohol dependency and family history of alcohol misuse compared with controls. CONCLUSION: Inherited variation in enzymes of ethanol metabolism may contribute to the pathogenesis of alcohol induced liver damage. This supports the presence of a genetic component in alcohol misuse.

Adult↗
PubMed2004

Classification of Giardia duodenalis parasites in Turkey into groups A and B using restriction fragment length polymorphism.

PCR-RFLP (restriction fragment length polymorphism) analysis was used to determine the relation of Giardia duodenalis Groups A and B. Of these, 17 (85%) were found as Group A in symptomatic cases; 22 (92%) were Group B in asymptomatic cases by using PCR-RFLP (p < 0.001). Interestingly, 5 (83%) were Group A in examination of endoscopy aspirates of symptomatic cases, as 5 (83%) were Group B in asymptomatic cases.

Animals↗
PubMed1991

[Oncogene amplification and inactivation of tumor suppressor genes in urological malignant tumors--the application of restriction fragment length polymorphism analysis].

We applied restriction fragment length polymorphism (RFLP) analysis to 24 cases of renal cell carcinomas (RCC), 18 cases of prostate adenocarcinomas (PC), and 11 cases of transitional cell carcinomas (TCC) in the renal pelvis to study the oncogene amplification and inactivation of tumor suppressor genes. All of the cases showed no amplification nor gross rearrangements of the Harvey ras, c-myc, c-fos, c-myb, EGFR and PDGFR. In contrast, RFLP analyses demonstrated allelic losses interpreted as inactivational events of TSGs among the tumor forms studied. RCC had allelic losses on the short arm of chromosome 3 (3p) (68%), the long arm of chromosome 18 (18q) (33%), Y chromosome (29%), and 17p (27%) at high frequencies. PC showed frequent allelic losses on 16q (67%), 8p (50%), 18q (43%), 10p (40%), and 10q (38%). TCC had allelic losses on 17p (73%), 11p (64%), and 9p (40%). It was likely that the cases with the more malignant grade tumor had the more allelic losses.

Gene Amplification↗
PubMed1989

HLA-DR beta, -DQ alpha, and -DQ beta restriction fragment length polymorphisms in multiple sclerosis.

Restriction fragment length polymorphism (RFLP) studies were performed on DNA from unrelated Caucasian patients with multiple sclerosis (MS) using cDNA probes to the HLA class II genes DR beta, DQ alpha, and DQ beta. In a study of 34 patients and 34 controls who were not matched for DR type, we found that the DQ beta allele-specific RFLP or allogenotype, termed DQ beta lb, which corresponds at the molecular level to the DQwl serotype, is preferentially associated with MS. A significant disease association with DR2 was demonstrated by serology but this was not confirmed using DR2/Dw2-specific RFLPs. We suggest that DQ beta lb is largely responsible for HLA-associated susceptibility to MS and that the apparent MS-DR2 serological association is due to the strong linkage disequilibrium between DR2 and DQ beta lb. Homozygosity of one of the two allelic bands of the DX alpha gene, usually termed the DX alpha lower (DX alpha L) band (which cross-hybridizes with the DQ alpha probe), correlated with reduced susceptibility to MS. Similarly a 5.3 kb band identified by the DQ alpha probe in Mspl digests showed a negative correlation with MS. In an analysis of 27 DR2+ controls and 26 DR2+ patients it was found that these individuals all had DR2/Dw2-specific RFLPs and all had identical DR2/Dw2-associated DQ beta (DQ beta lb) and DQ alpha (DQ alpha lb) allogenotypes. We detected no polymorphisms of DR beta, DQ alpha, or DQ beta genes among the DR2+ MS patients which distinguished them from normals.(ABSTRACT TRUNCATED AT 250 WORDS)

Alleles↗
PubMed1993

Mutation of H-ras is infrequent in bladder cancer: confirmation by single-strand conformation polymorphism analysis, designed restriction fragment length polymorphisms, and direct sequencing.

A series of 152 human bladder tumors, 14 bladder tumor cell lines, and 1 immortal urothelial cell line were examined by single-strand conformation polymorphism (SSCP) and designed restriction fragment.length polymorphism analyses for mutations in exons 1 and 2 of the H-ras gene. Nine tumors (6%) contained mutations. There was complete concordance between SSCP and restriction fragment length polymorphism analyses. Six mutations in exon 1 and three in exon 2 were identified by SSCP analysis. Subsequent restriction fragment length polymorphism analysis showed that of the exon 1 mutations, four were in codon 12 and two in codon 13, and all three exon 2 mutations were in codon 61. Eight mutations were confirmed by direct sequencing. One codon 13 mutation could not be identified by direct sequencing. Distinct strand mobility shifts detected by SSCP analysis identified specific point mutations, and in all cases, strands containing different mutations migrated differently. The base substitutions identified in these bladder tumors were diverse and included four transversions (three G-->T and one A-->T) and four transitions (two G-->A and two A-->G). This pattern of base substitutions is compatible with interactions of the urothelium with more than one class of environmental agent during bladder tumor development. No correlation was found between tumor grade and/or stage and the presence of H-ras mutation. We conclude that H-ras mutation does not play a role in the development of the majority of transitional cell tumors of the bladder.

Base Sequence↗
PubMed2001

Comparison of closely related orthopoxvirus isolates by random amplified polymorphic DNA and restriction fragment length polymorphism analysis.

The reliability and reproducibility of random amplified polymorphic DNA analysis (RAPD) was compared with restriction fragment length polymorphism (RFLP) by analysing three virus strains isolated from zoo animals in Berlin and three isolates which were cultivated from pets from Northern Germany. The RAPD technique was evaluated as a reliable tool with good reproducibility of the patterns for each virus strain investigated. Problems of interpretation due to inconsistent intensity of bands in different polymerase chain reaction runs may arise for less experienced personnel. The RAPD analysis can be performed within one working day and needs less DNA compared with RFLP so costs will be reduced. The obvious advantage of RFLP is that the pattern can be traced to the recognition site of the restriction enzyme whereas the RAPD primer sequence is not present in the orthopoxvirus genome at all. To the authors knowledge, the RAPD technique has never been applied in DNA viruses before and they conclude that this technique is a useful tool for the discrimination of closely related cowpoxviruses.

Animals↗
PubMed1995

Comparison of random amplified polymorphic DNA with restriction fragment length polymorphism as epidemiological typing methods for Mycobacterium tuberculosis.

Aim-To compare restriction fragment length polymorphism (RFLP) and random amplified polymorphic DNA (RAPD) methods for the epidemiological typing of Mycobacterium tuberculosis.Methods-Thirty one M tuberculosis cultures originating from patients in the Canton of Berne in Switzerland, which had previously been typed by RFLP, were subjected to RAPD analysis. Cultures were coded so that the investigators were blind to the RFLP results until RAPD analysis was complete.Results-The 31 cultures of M tuberculosis were divided into nine groups by RFLP and eight groups by RAPD. Generally there was good correlation between the groups identified by the two techniques, with the exception of strains that had only one copy of IS6110. Both methods subdivided isolates that were placed in a single group by the other method.Conclusions-RAPD analysis is quick, simple, and useful for the comparison of small numbers of isolates. RFLP is more reproducible and therefore better suited for the accumulation of RFLP fingerprints for long term local surveillance and large epidemiological studies.

Journal Article↗
PubMed2005

Improved assessment of denitrifying, N2-fixing, and total-community bacteria by terminal restriction fragment length polymorphism analysis using multiple restriction enzymes.

A database of terminal restriction fragments (tRFs) of the 16S rRNA gene was set up utilizing 13 restriction enzymes and 17,327 GenBank sequences. A computer program, termed TReFID, was developed to allow identification of any of these 17,327 sequences by means of polygons generated from the specific tRFs of each bacterium. The TReFID program complements and exceeds in its data content the Web-based phylogenetic assignment tool recently described by A. D. Kent, D. J. Smith, B. J. Benson, and E. W. Triplett (Appl. Environ. Microb. 69:6768-6766, 2003). The method to identify bacteria is different, as is the region of the 16S rRNA gene employed in the present program. For the present communication the software of the tRF profiles has also been extended to allow screening for genes coding for N2 fixation (nifH) and denitrification (nosZ) in any bacterium or environmental sample. A number of controls were performed to test the reliability of the TReFID program. Furthermore, the TReFID program has been shown to permit the analysis of the bacterial population structure of bacteria by means of their 16S rRNA, nifH, and nosZ gene content in an environmental habitat, as exemplified for a sample from a forest soil. The use of the TReFID program reveals that noncultured denitrifying and dinitrogen-fixing bacteria might play a more dominant role in soils than believed hitherto.

Bacteria↗
PubMed2003

Fidelity of select restriction endonucleases in determining microbial diversity by terminal-restriction fragment length polymorphism.

An evaluation of 18 DNA restriction endonucleases for use in terminal-restriction fragment length polymorphism (T-RFLP) analysis was performed by using richness and density indices in conjunction with computer simulations for 4,603 bacterial small-subunit rRNA gene sequences. T-RFLP analysis has become a commonly used method for screening environmental samples for precursory identification and community comparison studies due to its precision and high-throughput capability. The accuracy of T-RFLP analysis for describing a community has not yet been thoroughly evaluated. In this study, we attempted to classify restriction endonucleases based upon the ability to resolve unique terminal-restriction fragments (T-RFs) or operational taxonomic units (OTUs) from a database of gene sequences. Furthermore, we assessed the predictive accuracy of T-RFLP at fixed values of community richness (n = 1, 5, 10, 50, and 100). Classification of restriction endonuclease fidelity was performed by measuring richness and density for the entire database of T-RFs. Further analysis of T-RFLP accuracy for determining richness was performed by iterative, random sampling from the derived database of T-RFs. It became apparent that two constraints were influential for measuring the fidelity of a given restriction endonuclease: (i) the ability to resolve unique sequence variants and (ii) the number of unique T-RFs that fell within a measurable size range. The latter constraint was found to be more significant for estimating restriction endonuclease fidelity. Of the 18 restriction endonucleases examined, BstUI, DdeI, Sau96I, and MspI had the highest frequency of resolving single populations in model communities. All restriction endonucleases used in this study detected < or =70% of the OTUs at richness values greater than 50 OTUs per modeled community. Based on the results of our in silico experiments, the most efficacious uses of T-RFLP for microbial diversity studies are those that address situations where there is low to intermediate species richness (e.g., colonization, early successional stages, biofilm formation).

Bacteria↗
PubMed2003

Detection of isoniazid and rifampin resistance in Mycobacterium tuberculosis strains by single-strand conformation polymorphism analysis and restriction fragment length polymorphism.

Anti-Mycobacterium tuberculosis drug-resistance, mainly multi-drug resistance (MDR-TB), represents an important public health problem in several countries. Aim of our study is to identify the presence of these mutations in M. tuberculosis isoniazid- and rifampin-resistant strains isolated in our Institute; to evaluate linkage between type of mutation and level of resistance; to determine the usefulness of easy molecular techniques for rapid detection of such mutations on body specimens. Isoniazid- and rifampin-resistance was tested on 67 M. tuberculosis strains by Single-Strand Conformation Polymorphism (SSCP) and Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) assays, using HaeIII, PstuI, BsteII, BstuI enzymes. Drug-resistance of control strains was determined by cultural techniques (fluorimetry- BACTEC 9120). Cultural assay showed isoniazid- and rifampin-resistance in 6.12 and 2%, respectively (data confirmed by SSCP assay). Mutation of katG, linked to isoniazid resistance, was detected using BstuI enzyme, and mutation of rpoB, expression of reduced sensitivity to rifampin, using HaeIII. 15 body specimens, M. tuberculosis-positive to conventional assays, were tested by SSCP technique. Epidemiologic reports of numerous cases of tuberculosis due to MDR strains induce to detect quickly both Mycobacteria and drug-resistance, in order to start prompt effective therapy. On this basis, molecular assays are useful for a rapid therapeutic decision.

Antitubercular Agents↗
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↗
PubMed1995

DNA fingerprinting by random amplified polymorphic DNA and restriction fragment length polymorphism is useful for yeast typing.

Random amplified polymorphic DNA (RAPD) analysis was applied to genomic DNA from nineteen yeast strains belonging to the genera Saccharomyces and Zygosaccharomyces. Results obtained with five primers indicated that this technique is a powerful tool for yeast differentiation and identification. The data were consistent with those derived from restriction fragment length polymorphism (RFLP) using two S. cerevisiae DNA probes. We conclude that RAPD fingerprinting, combined with the analysis of RFLP, can provide unambiguous type assignment in yeasts.

DNA, Bacterial↗
PubMed1997

The usefulness of three biallelic restriction fragment length polymorphisms versus a polymorphic dinucleotide tandem repeat polymorphism at the low-density-lipoprotein receptor gene locus for diagnosis of familial hypercholesterolemia.

Indirect molecular diagnosis of familial hypercholesterolemia is possible based on genetic linkage analysis of DNA polymorphisms at the low-density-lipoprotein receptor gene locus in family studies. The use of biallelic restriction fragment length polymorphisms, however, is restricted by their low degree of heterogeneity, and therefore several of these markers have to be combined. To overcome these restrictions we examined the value and applicability of an (AT)n tandem repeat polymorphism at the 3' untranslated region of the gene, alone and in combination with three biallelic restriction fragment length polymorphisms in 35 independent healthy subjects and in familial hypercholesterolemia families with 23 parents and 52 children. For each family one of the parents had the clinical diagnosis of familial hypercholesterolemia. The probands were genotyped using the TaqI, HincII and NcoI restriction fragment length polymorphism and the (AT)n tandem repeat polymorphism of the gene. The heterozygosity index (0.60) and the polymorphism information content (PIC value) (0.53) of the ATn repeat polymorphism were higher compared to each single biallelic restriction fragment length polymorphism (heterozygosity index 0.26-0.54; PIC value 0.24-0.36). The combined PIC value of all three biallelic restriction fragment length polymorphisms (0.79) was comparable to the combination of the HincII and the ATn polymorphism (0.74). Using these two markers, a definitive molecular diagnosis could be made in 36 children from 15 parents compared to just 12 parents and their children using the three biallelic restriction fragment length polymorphisms. We conclude that the ATn tandem repeat polymorphisms is useful for indirect molecular diagnosis of familial hypercholesterolemia in affected families.

Chromosome Mapping↗
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↗
PubMed1996

Rapid identification of Campylobacter species by restriction fragment length polymorphism analysis of a PCR-amplified fragment of the gene coding for 16S rRNA.

Restriction fragment length polymorphism analysis of a PCR-amplified DNA fragment of the gene coding for 16S rRNA was performed on 148 previously characterized strains of Campylobacter, Helicobacter, Arcobacter, and Wolinella succinogenes and 13 Campylobacter-like isolates. These strains included clinical, animal, and environmental isolates. PCR amplification generated a 283-bp fragment from all species. The amplicon from each strain was digested with six restriction endonucleases (AccI, AvaI, DdeI, HaeIII, HpaII, XhoI). DdeI was useful for the initial grouping of the strains. Additional discrimination within the different DdeI groups was obtained with AccI, HaeIII, HpaII, and XhoI digestions. The PCR-restriction fragment length polymorphism analysis allowed for the discrimination of members of the genus Campylobacter from members of closely related genera and discrimination between Campylobacter species. The proposed method is simple and rapid and can be useful for the routine identification of Campylobacter-like organisms in clinical or epidemiologic studies.

Animals↗
PubMed2007

Residual polymerase activity-induced bias in terminal restriction fragment length polymorphism analysis.

Residual activity of polymerase chain reaction DNA polymerases in restriction analyses strongly affected genetic profiling based on terminal restriction fragment length polymorphisms. Artificial fragment sizes produced as a result of 5'-overhang restriction site fill-in and addition of a terminal A may bias genetic profiling and genotyping of microbial communities. Efficient removal of polymerases retained original fragment sizes and significantly reduced this profiling bias in soil bacterial communities.

Bacteria↗