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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↗

PubMed2005

Comparison between spoligotyping and IS6110 restriction fragment length polymorphisms in molecular genotyping analysis of Mycobacterium tuberculosis strains.

Spoligotyping was compared with RFLP fingerprinting analysis in the identification of Mycobacterium tuberculosis strains. Spoligotyping sensitivity was 97.6% with a specificity of 47%. The global probability for two strains clustered with spoligotyping to be clustered also with RFLP analysis was 33%; the probability for two strains clustered with RFLP analysis to be clustered also with spoligotyping analysis was 95%. However, comparing the two methods in five outbreak episodes, full concordance was evidenced between spoligotyping and RFLP. Moreover, we evaluated the presence of our 17 largest spoligotyping clusters in spoligotyping databases from Caribbean countries, London and Cuba. Only five out of 17 patterns were present in all the cohorts. The conditional probability comparing spoligotyping and RFLP methods related to these patterns resulted in very low concordance (range from 2 to 38%). In conclusion, we confirm that spoligotyping when used alone overestimates the number of recent transmission and does not represent a suitable method for wide clinical practice application. However, it allows to get a first good picture of strain identity in a new setting and in more localized or confined settings, the probability of reaching the same result compared to RFLP was 100% confirming the usefulness of spoligotyping in the management of epidemic events, especially in hospitals, prisons and close communities.

Bacterial Typing Techniques↗

PubMed2001

Prevalence of virulent Rhodococcus equi in isolates from soil collected from two horse farms in South Africa and restriction fragment length polymorphisms of virulence plasmids in the isolates from infected foals, a dog and a monkey.

The prevalence of virulent Rhodococcus equi in soil isolates from two horse farms in South Africa and nine clinical isolates from six foals, a foal foetus, a dog, and a monkey was investigated. The isolates were tested for the presence of virulence plasmid DNA and 15- to 17-kDa antigens by immunoblotting. Rhodococcus equi was isolated from almost all of the soil samples obtained from the two farms with 5.0 x 10(1) to 3.3 x 10(4) colony forming units per gram of soil. Virulent R. equi was isolated from three soil samples from one of the farms and appeared in 3.8% (three of 80 isolates), but not in any of the 182 isolates from the other farm. Of the three virulent R. equi isolates, one contained an 85-kb type I plasmid and two an 87-kb type I plasmid. Of nine clinical isolates from the foals, foal foetus, dog and monkey, five from the foals were virulent R. equi which expressed the virulence-associated antigens and contained a virulence plasmid 85-kb type I, and were all isolated from cases of pneumonia typical of that induced by R. equi in young foals living in widely separated areas in South Africa. The isolates from the other four foals, the dog and the monkey were avirulent R. equi.

Actinomycetales Infections↗

PubMed1996

Optimization of restriction fragment length polymorphism and single strand conformation polymorphism analysis for the detection of point mutations of ras oncogenes in paraffin-embedded tissues.

69 samples of formalin-fixed and paraffin-embedded tumor tissues (colon carcinomas n = 15, colon adenomas n = 15, transitional cell carcinomas of the urinary bladder n = 17, transitional cell papillomas of the urinary bladder n = 22) were investigated for point mutations of ras oncogenes using polymerase chain reaction (PCR) and nested-PCR followed by restriction fragment length polymorphism (RFLP) and single strand conformation polymorphism (SSCP), respectively. Results were proved by sequence analysis. Nested-PCR combined with SSCP analysis revealed five mutations of the Ki-ras oncogenes in five colon tumors. RFLP analysis revealed one point mutation in one sample of invasive transitional cell carcinomas. Using optimized PCR protocols, the methods described are applicable to paraffin- embedded tissues and offer a tool for mutation analysis in retrospective and prospective studies.

Base Sequence↗

PubMed1992

Distinct genetic groups of Giardia intestinalis distinguished by restriction fragment length polymorphisms.

The taxonomic status of the parasitic protozoal species Giardia intestinalis depends on the morphological similarity of all Giardia isolated from humans and the presumption that Giardia are host-specific. On the basis of electrophoretic data derived from examination of 26 enzyme loci in Australian isolates, it has been proposed that G. intestinalis is a species complex comprising three or four genetically distinct (but morphologically cryptic) species. These received the tentative designations of genetic groups I-IV (R. H. Andrews, M. Adams, P. F. L. Boreham, G. Mayrhofer & B. P. Meloni. International Journal for Parasitology 19, 183-190, 1989). In the present study, two unrelated DNA probes (one specific for a gene encoding a trophozoite surface protein, the other detecting a non-coding repetitive sequence within the G. intestinalis genome) were used in Southern hybridization analyses to examine 10 axenic isolates of G. intestinalis, established from diverse geographical regions in Australia, together with the Portland-1 isolate from the USA. Both probes identified every isolate unambiguously as belonging to one or other of two genetic clusters. Electrophoretic analysis of the same samples indicated that these clusters correspond to the previously defined genetic groups I and II. No heterogeneity was apparent within the seven group I isolates using either probe. However, when probed with the repetitive sequence, the four isolates belonging to group II exhibited small differences in banding patterns, suggesting that this group may be less homogeneous than group I.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗

PubMed1987

A common restriction fragment length polymorphism of the human apolipoprotein E gene and its relationship to type III hyperlipidaemia.

We report a common DNA polymorphism of the apolipoprotein E (apoE) gene detected with the enzyme HpaI. In an individual who is heterozygous for the polymorphism, two hybridising fragments of DNA, one of 50 kb (the H1 allele) and one of 20 kb (the H2 allele) are detected. In 54 controls the frequency of the rare allele is 0.38 (PIC value 0.36). We have also studied the frequency of the polymorphism in normolipidaemic and hyperlipidaemic individuals whose apo E protein typing is known. In 39 individuals with type III hyperlipidaemia and the apo E phenotype E2E2, the frequency of the H2 allele is 0.97. In contrast, the frequency of the H2 allele in normolipidaemic individuals with the E2E2 phenotype is closer to that found in the general population. Possible explanations for this are discussed.

Apolipoproteins E↗

PubMed2006

Analysis of Campylobacter spp. contamination in broilers from the farm to the final meat cuts by using restriction fragment length polymorphism of the polymerase chain reaction products.

We investigated the genotype diversity and dynamics of Campylobacter jejuni and Campylobacter coli in six commercial broiler farms during rearing and abattoir processing. In total, 223 C. jejuni and 36 C. coli strains isolated (on farm, transportation crates, carcasses after defeathering, and chicken wing meat at the end of the processing line) were subtyped by PCR-RFLP based on flagellin (fla typing) gene. Eleven (C. jejuni) and four (C. coli) different RFLP patterns were found. Multiple C. jejuni genotypes were identified in five out of six farms (except Farm 5). Furthermore, a clear tendency for dominance of particular genotypes was observed in almost all farms except Farm 3. Although diverse C. jejuni genotypes were isolated on the farms and transport crates, they were not detected in chicken wing cuts at the end of the processing line. We also observed varied distribution of types in different sampling stages both at the farm level and the processing environment. However, the interpretation of such fluctuations is precarious as new types occurred on some occasions, particularly during processing. Our results show that chicken wing meat contamination resulted mainly from farm strain carryover, and that the carcasses were probably contaminated during processing. In addition, the new strain types observed were isolated more frequently after defeathering as compared to other processing steps. Therefore, this stage, in addition to evisceration, is one of the critical control points in the processing line to prevent cross-contamination and for controlling the spread of campylobacters.

Animals↗

PubMed1995

Cyclins and autoimmunity: cyclin B1 gene expression and restriction fragment length polymorphism in lupus-prone mice.

Cyclin B1 is the major component of M-phase promoting factor that plays a major role in the G2/M transition of cell cycle. We examined the expression of cyclin B1 at the protein and mRNA levels in the thymus of 12-week-old autoimmune and normal mice. We found an abundance of cyclin B1 protein (58 kDa) in the thymus of lupus-prone MRL-lpr/lpr mice, whereas the level of this protein was negligible in other strains. The level of the predominant cyclin B1 mRNA (1.7 kb) species was not markedly different in these strains, suggesting post transcriptional modification of cyclin B1 in the thymus of MRL-lpr/lpr mice. Southern blot analysis of cyclin B1 gene showed multiple forms of cyclin B1-related sequences in various murine genomes. Flow cytometry showed a significantly higher level of cells in the G2/M phase and a significantly lower level in the S phase in thymocytes of MRL-lpr/lpr compared to that in normal BALB/c mice, indicating an alteration of cell cycle machinery in thymocytes of MRL-lpr/lpr mice. Taken together, these data show that an upregulation of cyclin B1 protein and accumulation of thymocytes at the G2/M phase in MRL-lpr/lpr mice might play an important role in the aberrant development of T cells in these mice.

Animals↗

PubMed2007

Characterization of a three bacteria mixed culture in a chemostat: evaluation and application of a quantitative terminal-restriction fragment length polymorphism (T-RFLP) analysis for absolute and species specific cell enumeration.

Growth dynamics of Pseudomonas aeruginosa, Burkholderia cepacia, and Staphylococcus aureus in a batch and chemostat, were investigated as a laboratory model system for persistent infections in cystic fibrosis. Most species-specific enumeration methods for mixed cultures are laborious or only qualitative, and therefore impede generation of quantitative data required for validation of mathematical models. Here, a quantitative T-RFLP method was evaluated and applied for specific and absolute cell number enumerations. The method was tested to be unbiased by quantitative sample composition and allowed reproducible enumerations of mixed cultures. For assay validation, samples of defined concentration containing one, two or three species were quantified. Logarithmically transformed absolute cell numbers of single-species dilutions were linear within a lower working range of 10(4)-10(6) cfu/mL (species-dependent) and an upper working range of 10(10) cfu/mL. Quantifications of single species (10(6)-10(10) cfu/mL) spiked with one or two other species agreed well with single species controls. Differences between slopes of first order linear regression of spiked and pure dilution series were insignificant. Coefficient of variation of defined mixed replicates was maximum 4.39%, of a three-species chemostat it was maximum 1.76%. T-RFLP monitoring of pure cultures in parallel shake flasks and of a three-species mixed chemostat gave very consistent results. Coexistence of at least two species after a time period equivalent to more than 33 volume exchanges was found. This result was not predicted from pure cultures clearly indicating the need for quantitative mixed culture experiments to better understand microbial growth dynamics and for mathematical model validation.

Biomass↗

PubMed1993

Cloning and restriction fragment length polymorphism analysis of a cDNA for swine PIT-1, a gene controlling growth hormone expression.

A partial swine cDNA which encodes the functional domain of PIT-1 was isolated by the polymerase chain reaction (PCR). The swine PIT-1 cDNA clone is 95% identical at the protein level to the rat Pit-1 gene. Thus, Pit-1's known function in control of rat growth hormone and prolactin expression is likely to be conserved in swine. This swine cDNA clone was used to investigate genetic variability at PIT-1 in several American and Chinese breeds. Polymorphic BamHI fragments were found in pure-bred Meishan animals (n = 13), but only monomorphic fragments in five American breeds (n = 36).

Amino Acid Sequence↗

PubMed1991

Restriction fragment length polymorphism in plants and its implications.

In the last decade RFLP analysis has evolved from an idea that seemed promising to a well-established tool that has led to fundamental advances in several fields. Construction of genetic maps has now become feasible in many organisms where it would previously have been impractical. Since genetic maps are of general utility for many sorts of biological research, they cannot fail to have a significant impact in the immediate future. As genetic maps become reconciled with physical maps in several plants, it will become possible to clone virtually any gene. For a plant breeder this will have the effect of broadening the gene pool available for plant improvement to include virtually all organisms, including animals and microorganisms. Much remains to be done, however. We need basic studies of the biochemistry, physiology, and genetics of plants and the insects and pathogens infesting them to be able to identify target genes for cloning. We need basic studies of transformation and gene expression to be able to have introduced genes expressed in transformed plants in the proper amounts and in the desired tissues. It must also be kept in mind that the best of our present technologies only suffice to clone and transform single genes. We will have to make another large jump in capabilities to be able to transfer QTL between plants. Since the most important agronomic traits are controlled by QTL, this effort will have to be undertaken. However, the future looks promising for plant breeding and RFLP analysis. The molecular genetic revolution now has every indication of being transferrable to practical problems such as plant breeding, and the first steps in this transferral have already occurred through the medium of RFLP analysis.

Breeding↗

PubMed2004

Characterization of a trinucleotide repeat sequence (CGG)5 and potential use in restriction fragment length polymorphism typing of Mycobacterium tuberculosis.

The genomes of 28 bacterial strains, including mycobacterial species Mycobacterium tuberculosis and Mycobacterium bovis, were analyzed for the presence of a special class of microsatellite, that of trinucleotide repeat sequences (TRS). Results of a search of all 10 possible TRS motifs (i.e., CCT, CGG, CTG, GAA, GAT, GTA, GTC, GTG, GTT, and TAT) with five or more repeating units showed that (CGG)(5) was highly represented within the genomic DNA of M. tuberculosis and M. bovis. Most of the (CGG)(5) repeats in the genome were within the open reading frames of two large gene families encoding PE_PGRS and PPE proteins that have the motifs Pro-Glu (PE) and Pro-Pro-Glu (PPE). (CGG)(5)-probed Southern hybridization showed that some mycobacterial species, such as Mycobacterium marinum, Mycobacterium kansasii, and Mycobacterium szulgai, possess many copies of (CGG)(5) in their genomes. Analysis of clinical isolates obtained from Tokyo and Warsaw with both IS6110 and (CGG)(5) probes showed that there is an association between the fingerprinting patterns and the geographic origin of the isolates and that (CGG)(5) fingerprinting patterns were relatively more stable than IS6110 patterns. The (CGG)(5) repeat is a unique sequence for some mycobacterial species, and (CGG)(5) fingerprinting can be used as an epidemiologic method for these species as well as IS6110 fingerprinting can. If these two fingerprinting methods are used together, the precise analysis of M. tuberculosis isolates will be accomplished. (CGG)(5)-based fingerprinting is particularly useful for M. tuberculosis isolates with few or no insertion elements and for the identification of other mycobacterial species when informative probes are lacking.

Base Sequence↗

PubMed2002

Quality of NAT2 genotyping with restriction fragment length polymorphism using DNA isolated from frozen urine.

In large studies and under field conditions common to epidemiological research, factors outside of and inside the laboratory can introduce misclassification of genetic susceptibility markers. Few reports have been made on the accuracy of genotyping individuals using DNA extracted from frozen urine that was stored for approximately 20 years. This study was performed to determine the reproducibility and accuracy of N-acetyltransferase 2 (NAT2) genotyping by RFLP analysis using DNA from stored urine. To obtain long-term frozen urine and blood samples from the same person, the databases of two large prospective studies were linked by name and date of birth. Six polymorphisms within the coding region of NAT2 were determined in 65 urine and blood samples after which, genotypes and imputed phenotypes (rapid, slow) were derived. To test reproducibility, all of the six polymorphisms were determined twice in 47 urine-blood pairs. Reproducibility of imputed phenotypes was 91.5% in urine samples and 97.9% in blood samples. To test accuracy, results for all six polymorphisms were compared between urine and blood DNA. All of the kappa's were at least 0.85 except one. Identical results for all six polymorphisms were seen in 78.5% of urine-blood pairs. Taking blood samples as a reference standard, rapid acetylators were classified as rapid in 97% of subjects (95% confidence interval, 90-100%), and slow acetylators were classified as slow also in 97% of subjects (95% confidence interval, 91-100%), when using urine. This study shows that stored urine samples can be used for DNA genotyping in large cohort studies, when blood samples are not available.

Aged↗

PubMed1995

Restriction fragment length polymorphisms at the apoprotein genes AI, CIII and B-100 and in the 5' flanking region of the insulin gene as possible markers of coronary heart disease.

Several sequence variations were examined for being endogenous "risk markers" in the development of CHD. The "markers" in this study included: the PstI-SstI RFLPs in the apo AI-CIII gene cluster, the EcoRI-MspI RFLPs in the apo B100 gene and the SstI RFLP in the 5' flanking region of the insulin gene. The study population comprised 700 individuals of German origin. A strong association of these "markers" to the disease phenotype predicts their loss in healthy individuals with ages above that of the prevalent incidence of CHD. In contrast, these "markers" should accumulate in diseased persons. A significant age-dependent selection was observed for the EcoRI RFLP in the apo B100 gene. This was the case when the allele and genotype frequencies of healthy old individuals were compared with those of newborns. In contrast, no RFLP showed significant differences in allele and genotype distributions between patients defined by coronary angiography and controls. In the group of patients, but not controls, several RFLP genotypes were found to be associated with significantly higher serum levels of cholesterol and triglycerides. This was true in the case of serum cholesterol comparing the genotypes S1S2 with those of S1S1 (p = 0.05) observed for the SstI polymorphic site in the 3' noncoding region of the apo CIII gene. Significantly higher levels of triglycerides were found within the heterozygous patients P1P2 (p = 0.045) and S1S2 (p = 0.02) than in the homozygotes P1P1 and S1S1 for the PstI-SstI RFLPs at the apo AI-CIII gene cluster.(ABSTRACT TRUNCATED AT 250 WORDS)

Aged↗

PubMed2000

Restriction fragment length polymorphism analysis of 16S rDNA and low molecular weight RNA profiling of rhizobial isolates from shrubby legumes endemic to the Canary islands.

Thirty-six strains of slow-growing rhizobia isolated from nodules of four woody legumes endemic to the Canary islands were characterised by 16S rDNA PCR-RFLP analyses (ARDRA) and LMW RNA profiling, and compared with reference strains representing Bradyrhizobium japonicum, B. elkanii, B. liaoningense, and two unclassified Bradyrhizobium sp. (Lupinus) strains. Both techniques showed similar results, indicating the existence of three genotypes among the Canarian isolates. Analysis of the combined RFLP patterns obtained with four endonucleases, showed the existence of predominant genotype comprising 75% of the Canarian isolates (BTA-1 group) and the Bradyrhizobium sp. (Lupinus) strains. A second genotype was shared by nine Canarian isolates (BGA-1 group) and the B. japonicum and B. liaoningense reference strains. The BES-5 strain formed an independent group, as also did the B. elkanii reference strains. LMW RNA profile analysis consistently resolved the same three genotypes detected by 16S ARDRA among the Canarian isolates, and suggested that all these isolates are genotypically more related to B. japonicum than to B. elkanii or B. liaoningense. Cluster analysis of the combined 16S ARDRA and LMW RNA profiles resolved the BTA-1 group with the Bradyrhizobium sp. (Lupinus) strains, and the BES-5 isolate, as a well separated sub-branch of the B. japonicum cluster. Thus, the two types of analyses indicated that the isolates related to BTA-1 conform a group of bradyrhizobial strains that can be clearly distinguishable from representatives of the tree currently described Bradyrhizobium species. No correlation between genotypes, host legumes, and geographic location was found.

Bradyrhizobium↗

PubMed1992

Restriction fragment length polymorphism analysis of ERBB2 oncogene by capillary electrophoresis.

Capillary electrophoresis (CE) with a sieving buffer containing ethidium bromide was applied to the detection of PCR-amplified RFLP samples. With CE, in contrast to agarose gel electrophoresis, run times are short, i.e., typically less than 30 min, the capillary can be re-used, and full automation is feasible. The addition of ethidium bromide to the buffer system in conjunction with a field amplification injection technique led to increased sample detectability and resolution. Migration time precision was better than 0.2% RSD with a approximately 12-bp resolution for the DNA fragment sizes of interest. RFLP samples were analyzed for homo- or heterozygosity based on the presence of 500- and/or 520-bp DNA fragments. Special software was used to correct for run-to-run migration time variations, thus facilitating genotype assignment.

DNA↗

PubMed2003

Social pairing and female mating fidelity predicted by restriction fragment length polymorphism similarity at the major histocompatibility complex in a songbird.

Female birds often copulate outside the pair-bond to produce broods of mixed paternity, but despite much recent attention the adaptive significance of this behaviour remains elusive. Although several studies support the idea that extra-pair copulations (EPCs) allow females to obtain 'good genes' for their offspring, many others have found no relationship between female mating fidelity and traits likely to reflect male quality. A corollary to the good genes hypothesis proposes that females do use EPCs to increase the quality of young, but it is the interaction between maternal and paternal genomes - and not male quality per se - that is the target of female choice. We tested this 'genetic compatibility' hypothesis in a free-living population of Savannah sparrows (Passerculus sandwichensis) by determining whether females mated nonrandomly with respect to the major histocompatibility complex (Mhc). During both the 1994 and 1995 breeding seasons, female yearlings (but not older birds) avoided pairing with Mhc-similar males (P < 0.005). The Mhc similarity between mates also predicted the occurrence of extra-pair young in first broods (P < 0.007) and covaried with estimates of genome-wide levels of similarity derived from multilocus DNA fingerprinting profiles (P = 0.007). The overall genetic similarity between adults tended to predict female mating fidelity, but with less precision than their Mhc similarity (P = 0.09). In contrast, females appeared insensitive to the size, weight or age of males, none of which explained variation in female mating fidelity. Taken together, these results are consistent with the hypothesis that females sought complementary genes for their offspring and suggest either that the benefits of heterozygosity (at the Mhc) drive female mating patterns or that the avoidance of inbreeding is an ultimate cause of social and genetic mate choice in Savannah sparrows.

Animals↗