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PubMed2002

[Variability of 6 Colombian strains of Trypanosoma cruzi with restriction fragment length polymorphisms (RFLP) and random amplification of polymorphic DNA (RAPD)].

Chagas disease, caused by the hemoflagellate Trypanosoma cruzi, is a public health problem in Colombia. Previous reports have indicated the presence of heterogeneity among parasite populations. Six Colombian T. cruzi strains were obtained that differed by host, geographical region and transmission cycle. The genetic variability of each was compared by random amplified polymorphic DNA (RAPD), and isoenzymes. A restriction fragment length polymorphism (RFLP) was extracted using the 1.2 kb unit encoding the parasite's H2A histone as a probe. Genetic distances between the isolates varied greatly, from 0.611 to 0.99 as determined by RAPD profiles (M13F and M13R primers), between 0 and 0.81 by RFLP profiles (5 endonucleases), and between 0.10 and 0.55 by isoenzymes (13 enzymatic systems). Genetic distance matrixes derived from each of the three methods showed that Colombian strains exhibit a high degree of genetic differentiation. This may account for the broad clinical spectrum of Chagas disease in Colombia.

Animals↗

PubMedDate not supplied

[Molecular typing by amplified fragment length polymorphism and PCR-restriction fragment length polymorphism , biotyping and antimicrobial susceptibility of Campylobacter jejuni].

Molecular typing systems have provided invaluable information for tracking infectious agents through the food chain. These tools have been essential for understanding the epidemiology of gastrointestinal infectious diseases, therefore providing essential and evidence-based information for appropriate interventions and preventative measures. Two such molecular typing techniques based on the polymerase chain reaction (PCR) that have been applied to the epidemiology of foodborne pathogens are, amplified fragment length polymorphism (AFLP) and restriction fragment length polymorphism (RFLP) analysis. Campylobacter is responsible for one of the most common bacteria foodborne gastrointestinal infections affecting humans, especially in developed countries. The object of this paper is to apply AFLP and RFLP analysis of the flagellin (flaA) gene to 18 isolates of Campylobacter jejuni from human sporadic cases in Italy. Results of these analyses were compared to the phenotypes of these isolates based on biotyping and antimicrobial resistance determinations. All isolates were typable by the four methods. The RFLP procedure was performed with DdeI and HinfI enzymes, and 12 and 8 distinct profiles respectively were recognised. AFLP analysis was more discriminatory, and recognised 16 different profiles. Results from AFLP were reproducible and applicable for definitive characterisation of C. jejuni isolated from different outbreaks. PCR-RFLP of the flaA gene represents a useful tool only to compare isolates within a single outbreak.

Anti-Bacterial Agents↗

PubMed2006

Cleaved amplified polymorphic sequence and amplified fragment length polymorphism markers linked to the fertility restorer gene in chili pepper (Capsicum annuum L.).

Cytoplasmic male sterility (CMS) in plants, which is due to failure to produce functional pollen, is a maternally inherited trait. Specific nuclear genes that sup-press CMS, termed fertility restorer (Rf) genes, have been identified in several plants. In this study, Rf-linked molecular markers in pepper (Capsicum annuum L.) were detected by bulked segregant analysis of eight amplified fragment length polymorphisms (AFLPs). Only AFRF8 was successfully converted to a cleaved amplified polymorphic sequence (CAPS) marker. This was named AFRF8CAPS and genotype determination using it agreed with that obtained with the original AFRF8. A linkage map with a total size of 54.1 cM was constructed with AFRF8CAPS and the seven AFLP markers using the Kosambi function. The AFRF8CAPS marker was shown to be closest to Rf with a genetic distance of 1.8 cM. These markers will be useful for fast and reliable detection of restorer lines during F(1) hybrid seed production and breeding programs in pepper.

Capsicum↗

PubMed1991

Polymorphic and monomorphic expression of arylamine carcinogen N-acetyltransferase isozymes in tumor target organ cytosols of Syrian hamsters congenic at the polymorphic acetyltransferase locus.

A number of human epidemiological investigations suggest a relationship between acetylator phenotype and the incidence and/or severity of tumors caused by exposure to arylamine carcinogens. Conclusions drawn from these investigations can be compromised by a variety of environmental and other genetic factors. To eliminate variability in these other factors, our laboratory recently completed construction of homozygous rapid (Bio. 82.73/H-Patr), heterozygous intermediate (Bio. 82.73/H-Patr/Pat(s)) and homozygous slow (Bio. 82.73/H-Pat(s)) acetylator congenic hamsters. The purpose of the present study was to assess the utility of this congenic hamster model for investigations into the relationship between acetylator genotype and arylamine carcinogenesis. We report the expression of acetylator genotype-dependent (polymorphic) and acetylator genotype-independent (monomorphic) N-acetyltransferase isozymes in hepatic cytosols. The hepatic polymorphic N-acetyltransferase isozyme isolated from the congenic hamsters expressed clearly acetylator-genotype dependent (Patr greater than Patr/Pat(s) greater than Pat(s)) N-acetylation towards p-aminobenzoic acid, 4-aminobiphenyl, 2-aminofluorene, p-aminophenol, 1-aminopyrene, 5-aminosalicylic acid, beta-naphthylamine, 3,4-dichloroaniline, 3,2'-dimethyl-4-aminobiphenyl and p-phenetidine. Acetylator genotype-dependent N-acetylation for a number of arylamines also was observed in liver, colon, kidney and urinary bladder cytosols derived from the congenic hamster lines, including arylamines highly carcinogenic to hamster colon and urinary bladders. It is concluded that the congenic hamster model will be useful in studies to delineate the role of acetylator genotype in the incidence or severity of arylamine tumors.

Animals↗

PubMed1989

HLA-DR beta-chain polymorphism. Second domain polymorphism reflects evolutionary relatedness of alleles and may explain public serologic epitopes.

Nucleic acid sequences of the second domain encoding exons and the signal sequence encoding exons are presented for a number of HLA-DR beta-chain alleles. There is less polymorphism in these regions than is found in the first domain encoding exon, a result expected from previous amino acid sequence data. The distribution of the polymorphisms follows a locus and supertype pattern. This permits an easy assignment of gene relatedness that is useful for ordering the events which have taken place in the first domain. The relative nonpolymorphism of the second domains within evolutionarily related haplotypes makes them likely candidates for encoding the epitopes recognized by public serologic reagents.

Alleles↗

PubMed1984

[Biochemical polymorphic systems in the population of immigrant inhabitants of the northeastern USSR. III. Selectivity of migration behavior with respect to the genotypes of polymorphic loci].

Genotype frequency correlation in individuals (1448 men and 1400 women) which left and those remained in the region was studied at 12 polymorphic loci (AcP, PGM, PGD, GPT, GLO-1, AK, Pp, Hp, Gc, Tf, ABO and Rh) in four years after the first examination. It is shown that the electivity of removal with respect to the genotypes of polymorphic systems studied determines the genetic structure specificity of the population. The men, in comparison with women, have more pronounced electivity and it is most considerable in the first years of dwelling under extreme conditions. It is ascertained that the electivity of the removal is a leading but not a sole factor determining the genetic structure specificity, because the significant differences in genotype frequencies between removed and remained individuals was found for some of the loci at which the frequency gradient depending on the duration of dwelling in the region was not found.

ABO Blood-Group System↗

PubMed1981

Investigation on the distribution of genetic polymorphisms in Greece. 3. Red cell enzyme polymorphisms and genetic distances G.

112 Greeks living in W. Germany and coming from various parts of Greece and 280 individuals from the Isle of Alonissos (northern Aegean Sea) have been typed for seven polymorphic red cell enzymes, namely red cell acid phosphatase (aP), phosphoglucomutase (PGM1) adenylate kinase (AK), 6-phosphogluconate dehydrogenase (6-PGD), esterase D (EsD), glutamic-pyruvic transaminase (GPT), and glyoxylase I (GLO). The gene frequencies obtained in these two samples are compared with the hitherto reported corresponding data from other Greek populations. Finally genetic distances (basing on six polymorphic serum protein and red cell enzyme systems) have been computed for seven Greek population samples. The results of these distance measurements are discussed.

Acid Phosphatase↗

PubMed1981

Investigations on the distribution of genetic polymorphisms in Greece. 2. Serum protein polymorphisms.

113 Greeks living in W. Germany and coming from various parts of Greece and 281 individuals from the Isle of Alonissos (northern Aegean Sea) have been typed for six serum protein polymorphisms, namely haptoglobin, group specific component (Gc), C 3, transferrin subtypes, Gm (1, 2, 3, 5, 13), and Inv (1). The gene frequencies obtained in these two samples are compared with the up to now reported data from other Greek populations. They show a marked genetic heterogeneity with respect to these polymorphisms.

Blood Proteins↗

PubMed1979

Polymorphism of apolipoprotein E. III. Effect of a single polymorphic gene locus on plasma lipid levels in man.

The two autosomal codominant alleles of the Apo E-N/D polymorphism, Apo En and Apo Ed, have a considerable influence on plasma lipid levels and distribution in man. Serum cholesterol levels are highest in phenotype Apo E-N, intermediate in phenotype Apo E-ND, and low in phenotype Apo E-D. Contrary VLDL-cholesterol is highest in phenotype Apo E-D, intermediate in heterozygotes, and lowest in phenotype Apo E-N. Serum-triglyceride, VLDL-triglyceride and the ratio of VLDL-cholesterol/serum-triglyceride are also intermediate in phenotype Apo E-ND between the two opposite homozygous groups. 10% of heterozygous Apo E-ND subjects exhibited a beta-VLDL subfraction compared to 0.8% in phenotype Apo E-N and 100% in Apo E-D. Hence the three phenotypic groups exhibit metabolic differences in vivo, and the gene Apo Ed has a mild dyslipoproteinemic effect even in a single dose. The Apo E-N/D polymorphism may therefore be a major influence on the occurrence of arteriosclerotic vascular disease in man.

Adult↗

PubMedDate not supplied

No point mutation but a codon 31ser-->arg polymorphism of the WAF-1/CIP-1/p21 tumor suppressor gene in nasopharyngeal carcinoma (NPC): the polymorphism distinguishes Caucasians from Chinese.

Mutational inactivation of the p53 tumor suppressor gene is an infrequent event in human nasopharyngeal carcinoma (NPC), a malignancy showing a high incidence in southern China and southeast Asia. To examine the possible involvement of an activated p53 pathway in nasopharynx carcinogenesis, we have screened primary NPC biopsies for possible point mutations in WAF-1/CIP-1/p21, an effector gene transcriptionally regulated by and functioning as a mediator of the p53 tumor suppressor gene. Mutations in WAF-1/CIP-1/p21 might mimic p53 mutations in tumors having wild-type p53 such as most NPCs. The mutational analysis of WAF/CIP/p21 by PCR-single strand conformational polymorphism-direct sequencing revealed no point mutation in 41 primary NPC biopsies. A codon 31ser-->arg polymorphism was, however, detected. A striking difference in the distribution of the serine (WAF-ser) and arginine (WAF-arg) forms of WAF-1/CIP-1/p21 was observed when normal healthy Caucasians and Chinese were compared (P < 0.0001). The majority of Caucasians examined were found to be homozygous for WAF-ser (89%, n = 65), while Chinese living in areas of high NPC incidence show a greater than 86% homozygous or heterozygous WAF-arg (Taiwan, n = 66; Hunan, n = 32). The two forms of WAF-1/CIP-1/p21 were examined for potential functional differences in their ability to inhibit cyclin-dependent kinases and tumor cell growth. No significant differences were detected. Furthermore, no association between WAF-1/CIP-1/p21 genotype and NPC risk was observed in a case-control study of 76 NPC cases and 66 normal controls conducted in Taiwan.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗

PubMed1995

[Follow-up of allogenic bone marrow graft with DNA polymorphisms. Use of two minisatellite MS31 and MS43 probes. Comparison with data of chromosomal polymorphisms].

OBJECTIVES: Allogenic bone marrow transplantation is widely used to treat many diseases of the haemopoietic system as well as metabolic disorders. Follow-up is essential to assess acceptance, rejection or post-graft relapse. This study was undertaken to evaluate the usefulness of the minisatellite probes MS31 and MS43 used as a routine follow-up test after bone marrow transplantation. METHODS: Twenty receivers of allogenic bone marrow transplants were followed-up. Two monoclonal minisatellite probes, MS31 and MS43, were used for comparison with the classical polymorphism methods. RESULTS: Fourteen cases of total chimeras, 3 cases of rejections and 3 cases of mixed chimeras were observed with the molecular probe techniques. In 19 of the 20 cases, this technique gave results compatible with classical polymorphism results. CONCLUSIONS: The minisatellite probes MS31 and MS43 were found to be sensitive, effective tests for bone marrow transplants which can be used in routine follow-up.

Adolescent↗

PubMed1996

Genetics of scnDNA polymorphisms in juvenile oysters (Crassostrea virginica). Part I: Characterizing the inheritance of polymorphisms in controlled crosses.

The amplification of DNA by polymerase chain reaction followed by restriction enzyme digestion was used to examine five anonymous single-copy nuclear DNA polymorphisms in 11 pair crosses for juvenile oysters (Crassostrea virginica). There was an overall 7% frequency of aberrant (non-Mendelian) offspring genotypes among 174 total pair-cross progeny. Strict Mendelian inheritance of alleles was observed for two of the five loci. Possible explanations for the aberrant offspring genotypes include nonamplifiable alleles owing to priming site polymorphism or aneuploidy, or paralogous amplification. Analysis of more pair crosses is needed to test these explanations.

Animals↗

PubMed1997

Detection of genomic polymorphisms among isolates of the intracellular bacterium Cowdria ruminantium by random amplified polymorphic DNA and Southern blotting.

Sixteen primers were successfully used in a RAPD assay to generate reproducible fingerprints for six isolates of Cowdria ruminantium, a tick-transmitted rickettsia of ruminants. Distinction between stocks was possible by using one or at most two primers. Two stocks were very similar although originating from widely distant geographical regions. A genetic distance tree was constructed by analysing 108 fragments in pairwise comparison between stocks. Three amplification fragments probed with C. ruminantium genomic DNA determined a restriction fragment length polymorphism which allowed the distinction between stocks except for the two stocks that had similar RAPD patterns. The potential of RAPD to determine the extent of genetic diversity of C. ruminantium and to develop probes or PCR primers for diagnostic purposes is discussed.

Blotting, Southern↗

PubMed2006

Polymorphism and pseudopolymorphism of salicaine and salicaine hydrochloride crystal polymorphism of local anaesthetic drugs, part V.

The local anaesthetic drug salicaine hydrochloride (hydroxytetracaine hydrochloride, 4-butylamino-2-hydroxybenzoic acid 2-dimethylaminoethyl ester hydrochloride, SLCHC) and the free-base salicaine (SLC) were characterized by thermal analysis, vibrational and solid-state NMR-spectroscopy, X-ray powder diffraction, X-ray single crystal structure analysis, and water vapor sorption analysis. Additionally, the crystal structures of the anhydrate mod. II degrees (monoclinic, space group P2(1)/n), the hydrated mod. I (triclinic, space group P(bar)1), and of the free base (SLC) in the form of the hemihydrate (triclinic, space group P(bar)1 are discussed. Mod. II degrees of the polymorphic SLCHC is the thermodynamically stable form at room temperature and is present in commercial products mostly contaminated with a hydrated form that is isomorphic with mod. I. Mod. II degrees crystallizes from most organic solvents and from the melt below 110 degrees C. Mod. I crystallizes from the melt at temperatures above 110 degrees C, and additionally appears on dehydration of the hydrated mod. I. A third polymorph monotropically related to mod. II degrees was found by freeze-drying. The free-base SLC was found to crystallize from ethanol/water as a triclinic hemihydrate.

Absorption↗

PubMed2007

Reversibility of enantiotropically related polymorphic transformations from a practical viewpoint: thermal analysis of kinetically reversible/irreversible polymorphic transformations.

Although enantiotropically related polymorphic transitions are thermodynamically reversible with temperature and pressure, they may be observed as either reversible or irreversible in practical investigations. This behavior may be explained simply by a difference in the energy barrier for the transition. However, this difference may have a significant effect on strategy in formulation development. This article summarizes the characteristics of enantiotropic transitions with reference to the literature. Also provided are careful investigations of polymorphic transitions by thermal analysis, which is the most promising method to investigate transition behavior.

Calorimetry, Differential Scanning↗

PubMed1996

Genetic Variability Among Isolates and Sexual Offspring of the Plant Pathogenic Fungus Calonectria morganii on the Basis of Random Amplification of Polymorphic DNA (RAPD) and Restriction Fragment Length Polymorphism (RFLP)

Thirty-two strains of the phytopathogenic mold Cylindrocladium scoparium (perfect state Calonectria morganii) isolated from ericaceous hosts and two specimens from the ATCC were examined by random amplification of polymorphic DNA (RAPD) and restriction fragment length polymorphism (RFLP). Five oligonucleotides were chosen as primers for differentiation of the isolates. RAPD patterns of the ATCC strains differed significantly from those of the field isolates. Diversity among field isolates was low. Results obtained in RFLP analysis, with telomere repeats of Neurospora crassa as a probe, were highly consistent with the RAPD data. Isolates were paired in all possible combinations; fertile perithecia occurred in only one combination, from which ascospores were analyzed by formal genetics and RAPD. A bipolar mechanism of homogenic incompatibility was found. Ascospore-derived strains were much more variable than field isolates. Phylogenetic trees suggested a correlation to the host plants from which the strains were isolated.

Journal Article↗

PubMed1998

Comparison of Randomly Amplified Polymorphic DNA with Amplified Fragment Length Polymorphism To Assess Genetic Diversity and Genetic Relatedness within Genospecies III of Pseudomonas syringae.

Recently, DNA pairing analyses showed that Pseudomonas syringae pv. tomato and related pathovars, including P. syringae pv. maculicola, form a genomic species (Pseudomonas tomato) (L. Gardan, H. L. Shafik, and P. A. D. Grimont, p. 445-448, in K. Rudolph, T. J. Burr, J. W. Mansfield, D. Stead, A. Vivian, and J. von Kietzell, ed., Pseudomonas syringae Pathovars and Related Pathogens, 1997). The genetic diversity of 23 strains belonging to this genomic species and 4 outgroup strains was analyzed with randomly amplified polymorphic DNA (RAPD) and amplified fragment length polymorphic (AFLP) techniques. Simple boiling of P. syringae cells was suitable for subsequent DNA amplification to obtain reliable patterns in RAPD and AFLP analyses. In general, the grouping of P. syringae strains by both analysis techniques corresponded well with the classification obtained from an RFLP analysis of ribosomal DNA operons, DNA pairing studies, and an analysis of pathogenicity data. However, two strains of P. syringae pv. maculicola produced distinct DNA patterns compared to the DNA patterns of other P. syringae pv. maculicola strains; these patterns led us to assume that horizontal transfer of DNA could occur between bacterial populations. Both techniques used in this study have high discriminating power because strains of P. syringae pv. tomato and P. syringae pv. maculicola which were indistinguishable by other techniques, including pathogenicity tests on tomato, were separated into two groups by both RAPD and AFLP analyses. In addition, data analysis showed that the AFLP method was more efficient for assessing intrapathovar diversity than RAPD analysis and allowed clear delineation between intraspecific and interspecific genetic distances, suggesting that it could be an alternative to DNA pairing studies. However, it was not possible to distinguish the two races of P. syringae pv. tomato on the basis of an analysis of the data provided by either the AFLP or RAPD technique.

Journal Article↗

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↗