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PubMed2003

Multilocus variable-number tandem repeat analysis distinguishes outbreak and sporadic Escherichia coli O157:H7 isolates.

Escherichia coli O157:H7 is a major cause of food-borne illness in the United States. Outbreak detection involves traditional epidemiological methods and routine molecular subtyping by pulsed-field gel electrophoresis (PFGE). PFGE is labor-intensive, and the results are difficult to analyze and not easily transferable between laboratories. Multilocus variable-number tandem repeat (VNTR) analysis (MLVA) is a fast, portable method that analyzes multiple VNTR loci, which are areas of the bacterial genome that evolve quickly. Eighty isolates, including 21 isolates from five epidemiologically well-characterized outbreaks from Pennsylvania and Minnesota, were analyzed by PFGE and MLVA. Strains in PFGE clusters were defined as strains that differed by less than or equal to one band by using XbaI and the confirmatory enzyme SpeI. MLVA was performed by comparing the number of tandem repeats at seven loci. From 6 to 30 alleles were found at the seven loci, resulting in 64 MLVA types among the 80 isolates. MLVA correctly identified the isolates from all five outbreaks if only a single-locus variant was allowed. MLVA differentiated strains with unique PFGE types. Additionally, MLVA discriminated strains within PFGE-defined clusters that were not known to be part of an outbreak. In addition to being a simple and validated method for E. coli O157:H7 outbreak detection, MLVA appears to have a sensitivity equal to that of PFGE and a specificity superior to that of PFGE.

Base Sequence↗
PubMed2006

IL1RN intron 2 polymorphism caused by variable number tandem repeats is associated with 1-year outcome in patients with ischaemic stroke.

BACKGROUND: Results of experimental and clinical studies suggest that recombinant human interleukin 1 receptor antagonist (rhIL1ra) may be a good new therapeutic agent for acute stroke. In humans, IL1ra is encoded by the IL1RN gene located on chromosome 2. OBJECTIVES: To report on the association between different genotypes of the variable number tandem repeat (VNTR) polymorphism within IL1RN, and disease severity and 1-year outcome in patients with ischaemic stroke. METHODS: IL1RN genotypes were evaluated using polymerase chain reaction in 391 patients with ischaemic stroke diagnosed according to the World Health Organization definition. The effects of IL1RN genotypes on severity of stroke at maximum impairment, and on the survival status and neurological and functional condition of patients at 7 days, 1 month, 3 months and 1 year after the onset, were evaluated. RESULTS: No relationship was found between IL1RN genotypes and severity of symptoms at the time of maximum impairment. Homozygotes for the IL1RN*2 allele showed less severe neurological and functional impairments when assessed after the time period between 7 days and 1 year after stroke compared with carriers of the other two IL1RN genotypes. Patients with at least one copy of the IL1RN*2 allele had increased risk of death during the first week, and patients homozygotic for this allele had increased risk of death within the first month after stroke. CONCLUSION: IL1RN intron 2 variable number tandem repeats polymorphism influences the clinical outcome in patients with ischaemic stroke. It may possibly modify effects of treatment with rhIL1ra in patients with acute stroke.

Brain Ischemia↗
PubMed2001

Pentanucleotide short tandem repeat locus DXYS156 displays different patterns of variations in human populations.

AIM: To establish a database for the pentameric short tandem repeat locus DXYS156 from worldwide populations for routine genotyping in forensic identity testing and evolutionary biology. METHODS: Using polymerase chain reaction with a newly designed primer pair, we analyzed 1,408 male and female samples from 28 populations representing four major geographic groups. RESULTS: We observed 11 different alleles, which we sequenced and used to construct an allelic ladder. CONCLUSION: DXYS156 displays a contrasting pattern of X-linked and Y-linked variation among geographic regions, and between X and Y chromosomes. This complex allele distribution may be forensically useful for the ethnic differentiation of unknown stains.

Alleles↗
PubMed1993

DNA polymorphism in cytokine genes based on length variation in simple-sequence tandem repeats.

The possibility of the involvement of cytokines in the genetic predisposition to various diseases has been suggested by a large variety of studies. However, the study of potential disease linkage of cytokine genes has been hampered by a lack of sufficiently polymorphic markers at the restriction fragment length polymorphism (RFLP) level. We have investigated the distribution, the length polymorphism, the informativeness, and the efficiency of analysis, of simple-sequence tandem repeats in the mouse cytokine genes. Highly polymorphic sequences have been identified in the IL-1 beta, IL-1ra, IL-2, IL-4, IL-5, IL-6, IL-7, and IFN-gamma genes. The utility and the value of these sequences as gene markers is exemplified by mapping the IL-7 gene to mouse chromosome 3 close to pgk-1ps3 and Car-2 loci and the IFN-gamma gene to chromosome 10 near the pg locus. Advantages of short tandemly repeated sequences as genetic markers are discussed in comparison with RFLPs.

Animals↗
PubMed1997

[Allelic polymorphism of short tandemly repeating sequences of the HUMF13A01 and HUMCD4 loci in Russian populations from Moscow and Tomsk].

In samples from populations of the cities of Moscow and Tomsk, analysis of allelic polymorphism of microsatellite loci HUMF13A01 and HUMCD4 was performed by polymerase chain reaction (PCR). Eight HUMCD4 alleles (115-165 bp) and nine alleles (180-230 bp) of locus HUMF13A01 were identified. In both populations, the distributions of allelic frequencies for these loci did not differ significantly. The distribution of observed genotype frequencies fitted Hardy-Weinberg equilibrium in both populations. Mendelian inheritance of these tandem repeats was demonstrated by analysis of two large families. Parameters of polymorphism information content (PIC) for the loci studied were detected; comparative analysis of allelic frequencies with similar data on several populations was performed. These short tandem repeats (STR) were proposed for use in personal identification and paternity tests.

Alleles↗
PubMed1998

Bovine submaxillary mucin contains multiple domains and tandemly repeated non-identical sequences.

A number of cDNA fragments coding for bovine submaxillary mucin (BSM) were cloned, and the nucleotide sequence of the largest clone, BSM421, was determined. Two peptide sequences determined from the purified apoBSM were found near the N-terminus of the mucin-coding region of BSM421. This clone does not contain a start or stop codon, but its 3' end overlaps with the 5' end of a previously isolated clone, lambdaBSM10. The composite sequence of 1589 amino acid residues consists of five distinct protein domains, which are numbered from the C-terminus. The cysteine-rich domain I can be further divided into a von Willebrand factor type C repeat and a cystine knot. Domains III and V consist of similar repeated peptide sequences with an average of 47 residues. Domains II and IV do not contain such sequences but are similar to domains III and V in being rich in serine and threonine, many of which are predicted to be potential O-glycosylation sites. Domain III also contains two sequences that match the ATP/GTP-binding site motif A (P-loop). Only beta-strands and no alpha-helices are predicted for the partial deduced amino acid sequence. Northern analysis of submaxillary gland RNA with the BSM421 probe detected multiple messages of BSM with sizes from 1.1 to over 10 kb. The tandemly repeated, non-identical peptide sequences of approx. 47 residues in domains III and V of BSM differ from the tandemly repeated, identical 81-residue sequences of pig submaxillary mucin (PSM), although both BSM and PSM contain similar C-terminal domains. In contrast, two peptide sequences of ovine submaxillary mucin are highly similar (86% and 65% identical respectively) to the corresponding sequences in domain V of BSM.

Amino Acid Sequence↗
PubMed1985

Unique sequences are interspersed among tandemly repeated elements in the murine gamma 1 switch segment.

Early in its differentiative pathway, a given B lymphocyte expresses immunoglobulin of the mu heavy chain class (IgM). Subsequent differentiative processes may involve rearrangement within the immunoglobulin heavy chain chromosomal locus to enable cells of the same lineage to synthesize immunoglobulins of other heavy chain classes (e. g. IgG, IgE or IgA), but with specificity for the same antigen as the original IgM molecule. Switch recombination, the molecular event which facilitates this chromosomal rearrangement, has been shown to occur between segments of DNA consisting of tandemly repeated unit sequences. These DNA segments have been functionally defined as switch regions. We have cloned the gamma 1 switch region from the BALB/c germline, and have demonstrated that significantly divergent sequence elements are interspersed among the tandemly repeated units characteristic of this switch region. We show that these unique elements exist in at least three copies within the switch segment, and discuss the implications of this novel and previously unreported primary structure.

Animals↗
PubMed1999

Characterization of a variable number tandem repeat region in the thiopurine S-methyltransferase gene promoter.

Characterization of the genetic polymorphism of thiopurine S-methyltransferase enzyme (TPMT; EC 2.1.1.67) is required because of its clinical importance for patients exposed to thiopurine drugs. A number of point mutations have already been characterized in exons and introns of the TPMT gene. Here we report the identification of a polymorphic locus within the promoter region of the gene. This polymorphism was detected by polymerase chain reaction - single strand conformation polymorphism analysis of DNA samples from 54 unrelated European individuals. A total of five alleles with length variations were distinguished through the 5'-flanking region involved in the TPMT gene expression. Sequence analysis revealed that these variations were due to a variable number of tandem repeats (VNTR), ranging from four to eight repeats. Each repeat consists of 17 or 18 bp units and contains putative binding sites for transcription factors. The most frequent alleles harbour four or five tandem repeats, a heterozygosity rate of 0.44 was calculated, and a stable Mendelian inheritance of alleles was demonstrated. Analysis of the effect of each VNTR allele on promoter activity of a reporter gene was further performed in various cell lines by transient transfection assay. A modulatory effect of VNTR alleles was observed in vitro, but the repeat polymorphism did not display a significative role in TPMT gene regulation in vivo. Further studies need to be carried out to support the hypothesis that VNTR may contribute to the large interindividual variations of TPMT activity.

Animals↗
PubMed2000

mtDNA tandem repeats in domestic dogs and wolves: mutation mechanism studied by analysis of the sequence of imperfect repeats.

The mitochondrial (mt) DNA control region (CR) of dogs and wolves contains an array of imperfect 10 bp tandem repeats. This region was studied for 14 domestic dogs representing the four major phylogenetic groups of nonrepetitive CR and for 5 wolves. Three repeat types were found among these individuals, distributed so that different sequences of the repeat types were formed in different molecules. This enabled a detailed study of the arrays and of the mutation events that they undergo. Extensive heteroplasmy was observed in all individuals; 85 different array types were found in one individual, and the total number of types was estimated at 384. Among unrelated individuals, no identical molecules were found, indicating a high rate of evolution of the region. By performing a pedigree analysis, array types which had been inherited from mother to offspring and array types which were the result of somatic mutations, respectively, could be identified, showing that about 20% of the molecules within an individual had somatic mutations. By direct pairwise comparison of the mutated and the original array types, the physiognomy of the inserted or deleted elements (indels) and the approximate positions of the mutations could be determined. All mutations could be explained by replication slippage or point mutations. The majority of the indels were 1-5 repeats long, but deletions of up to 17 repeats were found. Mutations were found in all parts of the arrays, but at a higher frequency in the 5' end. Furthermore, the inherited array types within the mother-offspring pair were aligned and compared so that germ line mutations could be studied. The pattern of the germ line mutations was approximately the same as that of the somatic mutations.

Animals↗
PubMed2000

Brucella abortus tandem repeated ATP-binding proteins, BapA and BapB, homologs of haemophilus influenzae LktB, are not necessary for intracellular survival.

Brucella abortus actively secretes materials and uptakes nutrients to maintain the survival and multiplication of the bacteria in host cells. ATP-binding cassette (ABC) transporters can uptake or secrete diverse materials across the bacterial membrane, and thus, ABC transporters may be important for survival of the pathogen in the host. In the present study, the B. abortus genes encoding tandem repeated Brucella ATP-binding proteins, BapA and BapB, were identified. The deduced amino acid sequences of these two genes place BapA and BapB into group 6 containing RTX toxin transporters and cyclic beta-1,2-glucan transporters, one of 25 ABC transporter ortholog groups. One of the ortholog group 6 proteins, Haemophilus influenzae LktB, shows the highest similarity and identity with these two Brucella proteins. To test the role of these putative tandem repeated ABC transporters in Brucella pathogenesis, a bap deletion mutant was constructed and used to infect murine RAW 264.7 macrophages and mice. The number of cfu from RAW 264.7 cells and spleens of BALB/c mice infected with wild type or the bap deletion mutant was similar during the course of infection, suggesting the bap genes are not necessary to maintain the pathogenesis of B. abortus, or alternative compensatory mechanisms may exist to permit the intracellular survival of B. abortus in vitro and in vivo. This is the first molecular approach to investigate the role of putative ABC transporters classified into ortholog group 6 in Brucella pathogenesis.

ATP-Binding Cassette Transporters↗
PubMed2002

Short tandem repeat polymorphism of the D2S1242 locus in a Japanese population.

Allele frequencies and sequence characteristics of the D2S1242 short tandem repeat (STR) locus were studied in a Japanese population sample. A total of 10 D2S1242 alleles and 34 genotypes were identified in 273 unrelated Japanese individuals. The five most common alleles detected had frequencies of over 10%. No deviations from Hardy-Weinberg equilibrium were found when the expected allele values were compared with the observed values. Sequence analysis of each allele showed a tetranucleotide polymorphism. Alleles 9 to 14 had different sequence structures than alleles 15 to 19. Allele 18 had a different sequence in the Japanese sample compared to an Austrian sample. The power of discrimination was 0.95. The present results demonstrate that the D2S1242 STR locus is a useful genetic marker in the Japanese population.

Alleles↗
PubMed2006

Polymorphisms at fifteen tetrameric short tandem repeat loci in three ethnic populations of Bengal, India.

The study presents allele frequency data at 15 tetrameric short tandem repeat (STR) loci (D3S1358, THO1, D21S11, D18S51, D5S818, D13S317, D7S820, D16S539, CSF1PO, vWA, D8S1179, TPOX, D2S1338, D19S433 and FGA) in three ethnic populations--Mahishya, Bauri and Namasudra of Bengal to evaluate their utility in Forensic testing and understanding population structure and dynamics. A total of 169 individuals were studied from the selected populations. On an average the combined power of discrimination and power of exclusion in these groups was found 0.97 and 0.99, respectively. The allele distribution pattern shows possible genetic admixture between these ethnic groups which could be attributed to their close geographical proximity and occupying almost similar position in the social hierarchy. This study suggests that the 13 Combined DNA Index System (CODIS) markers and two added markers named D2S1338, D19S433 are highly informative and therefore suitable in matching biological specimen in human identification and population genetic study.

DNA Fingerprinting↗
PubMed2003

[Application of short tandem repeat DNA in model of human-mouse cord blood transplantation].

OBJECTIVE: To evaluate the significance of applying short tandem repeat DNA in the model of human-mouse cord blood transplantation. METHODS: The techniques of STR-PCR and colony forming cell culture were used to examine the engrafting and influence of hematopoietic growth factor on process in the mice after transplantation of human cord blood (CB). RESULTS: 1. Human DNA expression was detected in the mice that had received tail-vein injection of human CB (1-5 x 10(7) MNC per mouse) but it was not detected in the mice that have received intraperitoneal injection of human CB. 2. Human CB transplanted in SCID mice could reconstitute the hematopoietic function of the mice; the expression level of human cell was not related with the use of hematopoietic growth factor. CONCLUSION: STR-PCR analysis provide a simple and accurate indication of engraftment in the model of human-mouse cord blood transplantation.

Animals↗
PubMed2000

Organization, nucleotide sequence, and chromosomal mapping of a tandemly repeated unit containing the four core histone genes and a 5S rRNA gene in an isopod crustacean species.

A tandemly repeated unit of 6553 bp containing a copy of the four core histone genes H2B, H2A, H3, and H4, and also a 5S rRNA gene, was amplified by PCR from genomic DNA of the isopod crustacean Asellus aquaticus. The linkage between 5S rRNA genes and histone genes has been so far observed in only one other organism, the anostrac crustacean Artemia salina. The gene cluster was cloned and sequenced. The histone genes, in their 3' flanking region, have the interesting feature of possessing two different mRNA termination signals, the stem-loop structure and the AATAAA sequence. A part of the PCR product was used as a probe in FISH experiments to locate the gene cluster on an inter-individually variable number of chromosomes from 6 to 12 per diploid cell, always in a terminal position and never associated with the heterochromatic areas. Fluorescence in situ hybridization (FISH) was also performed on preparations of released chromatin and the reiteration level of the gene cluster was determined as approximately 200-300 copies per haploid genome.

Animals↗
PubMed2006

Use of a multilocus variable-number tandem repeat analysis method for molecular subtyping and phylogenetic analysis of Neisseria meningitidis isolates.

BACKGROUND: The multilocus variable-number tandem repeat (VNTR) analysis (MLVA) technique has been developed for fine typing of many bacterial species. The genomic sequences of Neisseria meningitidis strains Z2491, MC58 and FAM18 have been available for searching potential VNTR loci by computer software. In this study, we developed and evaluated a MLVA method for molecular subtyping and phylogenetic analysis of N. meningitidis strains. RESULTS: A total of 12 VNTR loci were identified for subtyping and phylogenetic analysis of 100 N. meningitidis isolates, which had previously been characterized by pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing. The number of alleles ranges from 3 to 40 for the 12 VNTR loci; theoretically, the numbers of alleles can generate more than 5 x 1011 MLVA types. In total, 93 MLVA types were identified in the 100 isolates, indicating that MLVA is powerful in discriminating N. meningitidis strains. In phylogenetic analysis with the minimal spanning tree method, clonal relationships, established with MLVA types, agreed well with those built with ST types. CONCLUSION: Our study indicates that the MLVA method has a higher degree of resolution than PFGE in discriminating N. meningitidis isolates and may be a useful tool for phylogenetic studies of strains evolving over different time scales.

Bacterial Typing Techniques↗
PubMed2001

Genomic diversity at thirteen short tandem repeat loci in a substructured caste population, Golla, of southern Andhra Pradesh, India.

Genomic diversity based on 13 short tandem repeat (STR) loci was studied in seven population groups of a substructured Golla caste from Chittoor district in southern Andhra Pradesh, India. These groups are traditionally pastoral, culturally homogeneous, and strictly endogamous. Blood samples were drawn from 317 individuals from 30 Golla villages. The 13 STR loci analyzed in five standard multiplex polymerase chain reactions were: (1) CSF1R, TH01, and PLA2A; (2) F13A1, CYP19, and LPL; (3) D21S1446 and D21S1435; (4) D20S481, D20S473, and D20S604; and (5) D5S1453 and D6S1006. The average heterozygosity was found to be low among the Golla subgroups (0.64-0.70) in comparison to that of groups at the upper levels of the hierarchy. The coefficient of gene differentiation was found to be moderate (average GST = 0.031; range between 0.018 and 0.049 among the loci) when compared to that observed for a similar class of markers among populations with relatively higher levels of hierarchy, for example, among castes. It is, however, much higher when compared to the average observed for Indian caste and tribal populations, based on classical markers. Genetic distance measures revealed clusters of populations that are consistent with the known ethnohistorical and geographical backgrounds of the groups. We claim that these hypervariable markers are quite useful in understanding the process of substructuring within the Indian castes, leading to the formation of smaller breeding isolates, the basic Mendelian units within which microevolutionary forces operate.

Consanguinity↗
PubMed2005

Diversity of potential short tandem repeats in Mycobacterium leprae and application for molecular typing.

A recent advance in molecular typing for tracing the transmission of leprosy is the discovery of short tandem repeats (STRs) in Mycobacterium leprae. To substantiate polymorphic loci from STR as promising candidates for molecular typing tools in leprosy epidemiology, 44 STR loci including 33 microsatellites and 11 minisatellites were investigated among 27 laboratory strains by sequencing PCR products. Not all STRs were necessarily polymorphic. Thirty-two out of the 44 loci were polymorphic. Nine polymorphic loci were suitable for identifying genotypes according to the discriminatory capacity, stability, and reproducibility. All the strains were classified into independent genotypes by the selected nine loci. Three multi-case households were subjected to molecular typing. M. leprae obtained from household cases showed identical copy numbers by TTC triplet alone, but the isolates from one family contact case were divided into different genotypes by adding eight other polymorphic loci. The combination of information from multiple loci allows increasing levels of discrimination and it is likely that the generation and documentation of data will result in the choice of a potential molecular typing tool for leprosy epidemiology.

Animals↗
PubMed1993

Short tandem repeat loci: application to forensic and human remains identification.

The short tandem repeat (STR) locus ACTBP2 (common name SE33) was analyzed for its potential use in forensic and human remains identification. PCR amplification conditions were determined, and an allele-specific ladder was generated so that discrete alleles could be scored. The allele frequency distributions were determined for both Caucasian and Black populations. The frequency data meets Hardy-Weinberg expectations, and the allele distributions were similar from one racial group to another and between ethnic groups. SE33 analysis was subsequently used to confirm the identification of human remains for the Office of the Armed Forces Medical Examiners.

Alleles↗