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PubMed2003

A simple tandem repeat polymorphism is present in the eighth intron of FLJ12960, a possible queuine salvage enzyme gene.

The putative gene FLJ12960 was identified from sequence analysis of the human genome and predicted to be a member of the family of tRNA-guanine-transglycosylases for queuine biosynthesis by protein sequence similarity at the Zn-binding site (Locus Link #79691 at http://www.ncbi.nlm.gov/LocusLink/). FLJ12960 is immediately downstream of the Dopamine Receptor D3 (DRD3) gene. A Simple Tandem Repeat (STR) polymorphism was identified in intron 8 of the FLJ12960 gene. Primers designed to amplify the CA repeat detect 16 alleles from 121 to 151 base pairs, with a heterozygosity of 0.74.

Base Sequence↗
PubMed2004

Regions of high antigenicity within the hypothetical PPE major polymorphic tandem repeat open-reading frame, Rv2608, show a differential humoral response and a low T cell response in various categories of patients with tuberculosis.

The function of the PE/PPE families of proteins, which represent approximately 10% of the coding capacity of the Mycobacterium tuberculosis genome, has remained relatively unknown. We earlier described a PPE family member, Rv2430c, as an immunodominant antigen. We now report another PPE family gene, Rv2608, a member of the major polymorphic tandem repeat subfamily, for its ability to elicit a high humoral and a low T cell response. Rv2608 was also found to be polymorphic in different clinical isolates of M. tuberculosis, as determined by polymerase chain reaction-restriction fragment-length polymorphism analysis. A total of 51 clinically confirmed patients with tuberculosis (TB), belonging to 3 different categories--fresh infection (n=22), relapsed infection (n=21), and extrapulmonary infection (n=8)--and 10 healthy control subjects were included in the study. Recombinant Rv2608 protein showed positive reactivity to patients' serum samples. Enzyme-linked immunosorbent assays and T cell-proliferation assays with synthetic peptides corresponding to predicted regions of high antigenicity showed a predominantly humoral response in patients with relapsed TB. We additionally identified the Gly-X-Gly-Asn-X-Gly repeat motifs as being primarily responsible for eliciting a humoral immune response.

Amino Acid Sequence↗
PubMed2005

Rapid molecular typing of Burkholderia pseudomallei, isolated in an outbreak of melioidosis in Singapore in 2004, based on variable-number tandem repeats.

An increase in the number of reported melioidosis cases was observed in the first 4 months of 2004. These cases were associated with a significant increase in case-fatality rate compared with the past 5 years. In order to exclude the possibility of a single source, including the possibility of intentional release of Burkholderia pseudomallei, we applied a multiplex PCR-based multilocus variable-number tandem repeat (VNTR) assay to determine the clonality of the clinical isolates. Our investigation indicated that a total of 30 different VNTR types could be distinguished in the 32 clinical isolates of B. pseudomallei obtained during this period, thus indicating that infection was unlikely to have occurred from a single source. Our experience underscores the usefulness of a rapid strain typing method in augmenting an epidemiological investigation into an infectious disease outbreak, particularly at a time where the intentional use of biological agents is a potential threat to public health.

Bacterial Typing Techniques↗
PubMed2005

Short tandem repeat (STRs) and sex specific Amelogenin analysis of blood samples from neurosurgical female transfused patients.

Blood transfusion and its effects on DNA profiles of an individual is an important issue in the forensic context. In the present study, the effects of unfiltered whole male blood transfusion in seven female subjects were investigated by PCR-based assays on serial post-transfusion blood samples. PCR analysis of specific short tandem repeat (STR) primer pair to CSF1PO, TPOX, TH01, F13A01, FESFPS, vWA and sex specific Amelogenin loci for banding pattern of alleles generated from the pre- and post-transfusion of seven female recipients and their corresponding donors were studied. Pre- and post-transfusion DNA profiles of all the seven female recipients were found to be consistent with no evidence of the male and female donor genetic material. It is concluded that currently used PCR-based STRs and sex specific Amelogenin loci DNA profiling techniques in forensic science are reliable and informative for paternity and identity purposes in situations of transfusion of 1 or 2 U of unfiltered whole male and female blood (> 72 h old) to female recipient up to 24 h post-transfusion.

Alleles↗
PubMedDate not supplied

Correlation of minimal residual disease by assessing Wilms tumor gene expression and engraftment by variable number of tandem repeats in children with leukemia posthematopoietic stem cell transplantation.

An important measure to ensure successful follow-up in patients with allogeneic stem cell transplant is to evaluate for engraftment. Recent studies have shown that detecting minimal residual disease is important in order to predict early clinical relapse. We followed 88 leukemic patients with pre- and posttransplant Wilms tumor gene (WT1) levels to predict relapse and variable number of tandem repeats (VNTR) for engraftment. We have found that high pretransplant WT1 levels correlated significantly with relapse in all patient groups, but more significantly in the acute nonlymphoblastic leukemia (ANLL) patients. Posttransplant WT1 level correlated with VNTR status such that low WT1 is associated invariably with VNTR of 100% donor origin, while high WT1 is associated with VNTR of 20%. The association is significant in all patients, specifically in ANLL patients. In this preliminary study, we demonstrate that patients harboring detectable levels of WT1 prior to stem cell transplant have a higher chance of relapse, and posttransplant WT1 and VNTR status appeared to be dependent parameters predicting relapse when present in the posttransplant period. By combining 2 highly sensitive molecular techniques, we have found that this combined technique provided us with a promising alternative for overcoming the limitations imposed by each separate procedure. More studies are necessary before we can come to any significant conclusions.

Adolescent↗
PubMed2001

Haplotype variation in a mitochondrial tandem repeat of Norway spruce (Picea abies) populations suggests a serious founder effect during postglacial re-colonization of the western Alps.

Populations from 13 elevational transects of Norway spruce [Picea abies (L.) Karst] across the Alpine range were sampled to elucidate the geographical pattern of genetic variation in relation to postglacial re-colonization and to study elevational effects on haplotypic diversity. We assessed fragment length variation in a tandem repeat region of the mitochondrial (mt) nad1 intron 2. This maternally inherited genetic marker is suited to infer migration as it is dispersed by seed only. A total of 10 haplotypes was found, most of which were due to repeat copy number variation. An analysis of molecular variance (amova) showed that overall population differentiation was high (F(ST)=0.41), and it revealed a significant differentiation between monomorphic western and moderately to highly variable eastern Alpine populations. This phylogeographic pattern may be explained by a founder effect during postglacial re-colonization. An early arriving haplotype, assumed to originate from a western Carpathian refugium, could expand into suitable habitats, reducing the chances for establishment of subsequently arriving haplotypes. On the other hand, the high variation in populations within an Italian transect of the south-eastern Alps may be the consequence of merging migration pathways from and close distance to putative glacial refugia, most likely those assumed in the Carpathian mountains and on the Balkan peninsula or possibly in the central plains of Italy. An effect of elevation on haplotypic diversity was not evident, though a low, but significant, partition of total genetic variation was attributed to among-population variation in one Italian transect. Various factors, such as vertical seed dispersal and forest management, may account for blurring an otherwise established pattern of genetic variation on a small geographical scale.

Analysis of Variance↗
PubMed1989

Reductive acetylation of tandemly repeated lipoyl domains in the pyruvate dehydrogenase multienzyme complex of Escherichia coli is random order.

In vitro deletion and site-directed mutagenesis of the aceF gene of Escherichia coli was used to generate dihydrolipoamide acetyltransferase (E2p) polypeptide chains containing various permutations and combinations of functional and non-functional lipoyl domains. A lipoyl domain was rendered non-functional by converting the lipoylatable lysine residue to glutamine. Two- and three-lipoyl domain E2p chains, with lipoyl-lysine (Lys244) substituted by glutamine in the innermost lipoyl domains (designated +/- and +/+/-, respectively), and similar chains with lipoyl-lysine (Lys143) substituted by glutamine in the outer lipoyl domains (designated -/+ and -/-/+), were constructed. In all instances, pyruvate dehydrogenase complexes were assembled in vivo around E2p cores composed of the modified peptide chains. All the complexes were essentially fully active in catalysis, although the complex containing the -/-/+ version of the E2p polypeptide chain showed a 50% reduction in specific catalytic activity. Similarly, active-site coupling in the complexes containing the +/-, +/+/- and -/+ constructions of the E2p chains was not significantly different from that achieved by the wild-type complex. However, active-site coupling in the complex containing the -/-/+ version of the E2p chain was slightly impaired, consistent with the reduced overall complex activity. These results indicate that during oxidative decarboxylation there is no mandatory order of reductive acetylation of repeated lipoyl domains within E2p polypeptide chains, and strongly suggest that the three tandemly repeated lipoyl domains in the wild-type E2p chain function independently in the pyruvate dehydrogenase complex.

Acetylation↗
PubMed2004

A simple Duplex-PCR to evaluate the DNA quality of anthropological and forensic samples prior short tandem repeat typing.

Typing of DNA from ancient or otherwise highly degraded material, e.g. formalin fixed tissues, can be difficult, time consuming and costly. Very often, genetic typing is not possible at all. We present an inexpensive and easy to use Duplex-PCR that amplifies a 164 bp fragment specific for nuclear DNA together with a 260 bp mitochondrial DNA fragment and that can be employed as a pretest prior to short tandem repeat (STR) typing. All together, we analyzed DNA from 20 ancient bones, 20 formalin fixed tissues and 20 other forensic samples in different concentrations. Each sample that failed in the presented Duplex-amplification was also negative for STR typing, while samples that showed strong and clear signals in the Duplex-PCR led to reproducible genetic profiles using the multiplex kits AmpFLSTR Identifiler and Powerplex ES. The Duplex-PCR worked as a reliable indicator of DNA quality in the sample.

Bone and Bones↗
PubMed2005

DNA hypomethylation reduces homologous pairing of inserted tandem repeat arrays in somatic nuclei of Arabidopsis thaliana.

Fluorescent chromatin tagging makes possible tracking of specific loci in vivo and in situ. Loci tagged by the lac operator (lacO)/GFP-LacI/Nuclear Localization Signal (NLS) system show rapid motility and constrained chromatin dynamics in somatic nuclei of a transgenic line, designated EL702C, in Arabidopsis thaliana. The tagged loci associated with each other significantly more often than expected at random, due to homologous pairing of the lacO tandem repeat arrays. Furthermore, these arrays associated significantly more often than average euchromatic regions with heterochromatic chromocenters (CCs). We show now that the inserted lacO array in this transgenic line became strongly methylated at CG sites in the T3 generation, which can be reversed upon transfer into the mutant backgrounds of decrease in DNA methylation 1 (ddm1) and methyltransferase 1 (met1). Concomitantly, the tagged loci showed lower association frequencies as compared with the transgenics in wild-type background, which is correlated with a significant decrease in allelic and ectopic pairing of the lacO repeat arrays as visualized by fluorescence in situ hybridization. In contrast, the preferential association of the lacO arrays with heterochromatin, locus mobility in somatic nuclei and transcription of neighboring transgenes were not altered by reduced DNA methylation in ddm1 and met1 backgrounds. Our results show that repeat arrays can activate hypermethylation of the inserted locus that correlates with high frequencies of homologous pairing in somatic cells. In contrast, the preferential association of these inserted arrays with CCs in plant cells occurs through another mechanism.

Arabidopsis↗
PubMed2001

Uniform 13C/15N-labeling of DNA by tandem repeat amplification.

An optimized procedure has been described for the large-scale production of stable isotopeenriched duplex oligonucleotides of designed sequence. Large-scale production of labeled nucleotide triphosphates can be produced in this procedure simultaneously with labeled proteins, thereby providing synthetic dNMP precursors at no additional cost. The procedure is robust, with a minimum product:template yield of 800:1 overall, and produces > 99% single-length product. Tandem repeat PCR amplification is a general approach to large scale synthesis of duplex oligonucleotides and may have applications to both NMR and X-ray methods, particularly for product lengths in excess of 25 base pairs where failed sequences from solid-phase synthesis can be difficult to remove chromatographically. A drawback of the present approach is that the product is a duplex of two equal-length strands, making single-stranded products more difficult to prepare. For this reason, it could be preferable to produce single-stranded products by the [figure: see text] method of Zimmer and Crothers. Although a single base type can be selectively enriched in this approach, chemical synthesis will provide greater flexibility for labeled DNAs requiring site-specific labels at only one or a small number of nucleotide positions in the sequence. Therefore, maximum flexibility in labeling patterns can be realized by judicious choice of labeling method appropriate to the type of DNA product and extent of isotopic enrichment desired.

Base Sequence↗
PubMed2006

Population data from sub-populations of the Northern Territory of Australia for 15 autosomal short tandem repeat (STR) loci.

It is a requirement that forensic DNA profiling evidence be accompanied by an estimation of its weight, in order that the court can assign an appropriate probative value to the evidence during legal proceedings. There are various models by which this estimation can be made, but each relies on approximations of the allele frequencies in the relevant population. It is also important to assess relevant population genetic features of the available data. This report provides allele frequencies and estimates of common population genetic parameters for the major sub-populations of the Northern Territory of Australia genotyped at 15 autosomal short tandem repeat (STR) loci.

Australia↗
PubMed2004

Short tandem repeat polymorphism in a novel esophageal cancer-related gene (ECRG2) implicates susceptibility to esophageal cancer in Chinese population.

We have previously cloned and identified a novel esophageal cancer related gene 2 (ECRG2; GenBank Accession Number AF268198), which is down-regulated in esophageal squamous cell carcinoma (ESCC) and involved in the induction of the apoptosis in esophageal cancer cell lines. In the present study, we have found a short tandem repeat (STR) polymorphism in the noncoding region of the exon 4 of the ECRG2 gene by using PCR-denaturing high-performance liquid chromatography (DHPLC). Three STR genotypes, TCA3/TCA3, TCA3/TCA4 and TCA4/TCA4 were revealed and confirmed by DNA sequencing analysis. A total of 661 objects including 228 patients with ESCC and 373 normal controls were analyzed to investigate the impact of this ECRG2 STR polymorphism on risk of ESCC in case-control studies. Genotypes were determined in 231 controls and 162 cases from Beijing, which is a low risk area of ESCC, and in 142 controls and 126 cases from Linxian, a well-known high-risk area of ESCC. In both of the Beijing and Linxian population, subjects who carried the TCA3/TCA3 genotype were at an increased risk of ESCC compared to those carrying the TCA4/TCA4 genotype, with the adjusted odds ratios (ORs) being 2.05 [95% confidence interval (CI), 1.02-4.06] for the subjects from Beijing and 4.40 (95% CI, 1.93-10.01) for the subjects from Linxian. Furthermore, comparison of the genotype distributions among other cancer sites might suggest that risk of the ECRG2 STR polymorphism might be specific to the esophagus. These findings indicate for the first time that the ECRG2 STR is a genetic susceptibility factor for ESCC and the TCA3/TCA3 allele might play a role in the development of this cancer.

Aged↗
PubMed2005

Application of quantitative fluorescent PCR with short tandem repeat markers to the study of aneuploidies in spontaneous miscarriages.

BACKGROUND: Aneuploidies involve approximately 80% of chromosomal anomalies found in spontaneous miscarriages. Since cytogenetic studies show high rates of failure, we have incorporated the quantitative fluorescent polymerase chain reaction (QF-PCR) technique to the study of numerical chromosome anomalies in miscarriages. METHODS: Multiplex and simple QF-PCR assays have been performed on 160 miscarriage and 34 parental DNA samples analysing specific short tandem repeat (STR) markers for chromosomes 2, 7, 13, 15, 16, 18, 21, 22 and X. Cases successfully karyotyped were used as controls in our study. RESULTS: While maternal contamination could be detected in such cases, a molecular result was obtained for 94% of miscarriages without a cytogenetic one. Thirty-six per cent of them were diagnosed with numerical chromosome anomalies. Parental origin of the extra chromosome and the error stage of meiosis could be also determined. CONCLUSIONS: QF-PCR represents a useful and reliable tool to diagnose aneuploidies in spontaneous miscarriages. It provides information about parental and meiotic origin of anomaly, allowing an appropriate genetic counselling.

Abortion, Spontaneous↗
PubMed2004

Tandem repeat of a seven-bladed beta-propeller domain in oligoxyloglucan reducing-end-specific cellobiohydrolase.

Oligoxyloglucan reducing-end-specific cellobiohydrolase (OXG-RCBH; EC 3.2.1.150) is an exoglucanase that recognizes the reducing end of oligoxyloglucan and releases two glucosyl residue segments from the main chain. The X-ray crystal structure of OXG-RCBH determined at 2.2 A resolution reveals a unique feature of this enzyme; OXG-RCBH consists of a tandem repeat of two similar domains, which are both folded into seven-bladed beta-propeller structures. The sequence alignment of the propeller blades, based on the structure, indicates that a weak repeat of the amino acid sequence occurred seven times to construct each domain. There is a cleft that can accommodate the substrate oligosaccharide between the two domains, which is a putative substrate binding subsite. Mutation of either Asp35 or Asp465, located in the putative catalytic center, to Asn resulted in a protein with no detectable catalytic activity, indicating the critical role of these amino acids in catalysis.

Amino Acid Sequence↗
PubMed2005

A comparison of fluorescent in situ hybridization and multiplex short tandem repeat polymerase chain reaction for quantifying chimerism after stem cell transplantation.

BACKGROUND AND OBJECTIVES: Despite the great utility of chimerism analysis after allogeneic stem cell transplantation, a gold standard method for its quantification has not yet been defined. The objective of the present investigation was to compare the sensitivity (detection limit) and the quantification accuracy of fluorescent in situ hybridization with specific probes for the sex chromosomes (XY-FISH) and multiplex short tandem repeat polymerase chain reaction (STR-PCR) revealed by capillary electrophoresis for the quantification of chimerism after stem cell transplantation. DESIGN AND METHODS: A first experiment was performed on two sets of artificial cell mixtures from two sex-mismatched healthy donors mixed in different proportions (% male: 100, 75, 50, 25, 10, 5, 3, 1, 0.1, 0). In a second experiment, 58 samples obtained from 10 selected patients with different clinical courses and chimerism evolution after sex-mismatched stem cell transplantation, which had been studied by XY-FISH, were retrospectively analyzed by STR-PCR. In a third experiment, 60 unselected prospective samples belonging to 15 patients (5 of whom had also been included in the retrospective study) were analyzed by both XY-FISH and STR-PCR. RESULTS: Both techniques showed high quantification accuracy and were highly reproducible. The sensitivity of both approaches reached 1% under standard conditions. Moreover, the use of long injection times for the capillary electrophoresis (30 and 50s vs. the standard 10s) resulted in an increase of sensitivity of the STR-PCR assay up to 0.1%, which has interesting clinical implications. INTERPRETATION AND CONCLUSIONS: Considering the high sensitivity and quantification accuracy of multiplex STR-PCR and the fact that this assay is sex-independent and can be applied to virtually all patients, STR-PCR could be considered as the method of choice for chimerism quantification after stem cell transplantation when high sensitivity is not a requirement.

Adolescent↗
PubMed1990

Polyproline, beta-turn helices. Novel secondary structures proposed for the tandem repeats within rhodopsin, synaptophysin, synexin, gliadin, RNA polymerase II, hordein, and gluten.

Seven proteins each contain 8 to 52 tandem repeats of a unique class of oligopeptide. The consensus peptide for each is rhodopsin Tyr Pro Pro Gln Gly synaptophysin Tyr Gly Pro Gln Gly synexin Tyr Pro Pro Pro Pro Gly gliadin Tyr Pro Pro Pro Gln Pro RNA polymerase II Tyr Ser Pro Thr Ser Pro Ser hordein Phe Pro Gln Gln Pro Gln Gln Pro gluten Tyr Pro Thr Ser Pro Gln Gln Gly Tyr Although there is obvious variation of sequence and of length, the penta- to nonapeptides share an initial Tyr (or Phe) and have high Pro contents and abundant Gly, Gln, and Ser. We have evaluated helical models that both recognize the uniqueness of these sequence repeats and accommodate variations on the basic theme. We have developed a group of related helical models for these proteins with about three oligopeptide repeats per turn of 10-20 A. These models share several common features: Most of the phi dihedral angles are -54 degrees, to accommodate Pro at all positions except the first (Tyr). Except for the beta-turns, most psi dihedral angles are near +140 degrees as found in polyproline. Each oligopeptide has at least one beta-turn; several have two. Some contain a cis-Tyr, Pro peptide bond; a few have a cis-bond plus one beta-turn. Tyr side chains vary from totally exposed to buried within the helices and could move to accommodate either external hydrophobic interactions or phosphorylation. The several related structures seem to be readily interconverted without major change in the overall helical parameters, and therein may lie the key to their functions.

Amino Acid Sequence↗
PubMed1996

Polymorphism and concerted evolution in a tandemly repeated gene family: 5S ribosomal DNA in diploid and allopolyploid cottons.

5S RNA genes and their nontranscribed spacers are tandemly repeated in plant genomes at one or more chromosomal loci. To facilitate an understanding of the forces that govern 5S rDNA evolution, copy-number estimation and DNA sequencing were conducted for a phylogenetically well-characterized set of 16 diploid species of cotton (Gossypium) and 4 species representing allopolyploid derivatives of the diploids. Copy number varies over twentyfold in the genus, from approximately 1,000 to 20,000 copies/2C genome. When superimposed on the organismal phylogeny, these data reveal examples of both array expansion and contraction. Across species, a mean of 12% of nucleotide positions are polymorphic within individual arrays, for both gene and spacer sequences. This shows, in conjunction with phylogenetic evidence for ancestral polymorphisms that survive speciation events, that intralocus concerted evolutionary forces are relatively weak and that the rate of interrepeat homogenization is approximately equal to the rate of speciation. Evidence presented also shows that duplicated 5S rDNA arrays in allopolyploids have retained their subgenomic identity since polyploid formation, thereby indicating that interlocus concerted evolution has not been an important factor in the evolution of these arrays. A descriptive model, one which incorporates the opposing forces of mutation and homogenization within a selective framework, is outlined to account for the empirical data presented. Weak homogenizing forces allow equivalent levels of sequence polymorphism to accumulate in the 5S gene and spacer sequences, but fixation of mutations is nearly prohibited in the 5S gene. As a consequence, fixed interspecific differences are statistically underrepresented for 5S genes. This result explains the apparent paradox that despite similar levels of gene and spacer diversity, phylogenetic analysis of spacer sequences yields highly resolved trees, whereas analyses based on 5S gene sequences do not.

Base Sequence↗
PubMed1989

Inefficient expression in rat cells of transforming gene of BK virus with 68-bp tandem repeats in the viral promoter-enhancer.

Large-plaque BK virus (wt-501), which has three 68-bp tandem repeats in the viral promoter-enhancer, is not transforming for rat cells, whereas the minute-plaque mutant (dl-504) with only one 68-bp element is. We tested the BKV wt-501 and dl-504 promoter-enhancers for their ability to activate the heterologous and homologous genes in rat 3Y1 cells. The 501 promoter-enhancer activated expression of the chloramphenicol acetyltransferase gene and the neomycin-resistance gene more efficiently than the 504 promoter-enhancer. The 501 enhancer could not allow the efficient expression of BK virus T-antigen gene, whereas the 504 enhancer could. The wt-BKV enhancer with three 68-bp repeats seemed to function positively on the heterologous genes but negatively on the homologous transforming gene in rat cells. The sequence causing the suppressive effects by duplication was confined within the 29-bp segment containing two SV40 enhancer core homologies in the 68-bp element. The results show that inability of wt-BKV to transform rat cells is ascribable to inefficient T-antigen gene expression caused by the duplication in the enhancer and by the surrounding or downstream DNA sequence.

Animals↗