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Tandem repeats of T helper epitopes enhance immunogenicity of fusion proteins by promoting processing and presentation.

Empirical findings have shown that recombinant chimeric proteins may be made more immunogenic if T helper epitopes are incorporated as tandem repeats. In the present study we investigated the mechanisms responsible for the enhanced immunogenicity of fusion proteins composed of the heat-stable enterotoxin of enterotoxigenic E. coli (STa) linked to multiple copies of the ovalbumin323-339 T helper epitope (ova) and a connecting dimer of an Ig-binding region of Staphylococcus aureus protein A (ZZ), which were previously shown to stimulate strong anti-STa titres in mice. We used B cell and macrophage cell lines as APC and IL-2 production by ova-specific T cells as our read-out system. Fusion proteins containing four repeated T helper epitopes were found to be the most immunogenic and resulted in 50-fold higher IL-2 production than constructs with a single T helper epitope. Under limiting APC conditions the construct with four epitopes was the best inducer of IL-2, indicating that this construct was most effectively processed by the APC. Analysis of IL-2R alpha expression by flow cytometry confirmed that four copies gave the highest frequency of activated T cells in culture, indicating a direct correlation between ability to activate T cells and IL-2 production in culture. Also in vivo, the fusion protein with four epitopes exhibited the strongest T cell priming effect. Moreover, both in vitro and in vivo, the ZZ construct was found to serve as an efficient means for targeting of the fusion proteins to B cells, thereby allowing access to the Ig receptor uptake pathway for Ag. The present study provides direct evidence that fusion proteins can be constructed to optimize processing in the individual APC and enhance activation of clonal T cells.

Animals↗

High frequencies of short frameshifts in poly-CA/TG tandem repeats borne by bacteriophage M13 in Escherichia coli K-12.

Slipped-strand mispairing (SSM) may play an major role in repetitive DNA sequence evolution by generating large numbers of short frameshift mutations within simple tandem repeats. Here we examine the frequency and size spectrum of frameshifts generated within poly-CA/TG sequences inserted into bacteriophage M13 in Escherichia coli hosts. The frequency of detectable frameshifts within a 40 bp tract of poly-CA/TG is greater than one percent and increases more than linearly with length, being lower by a factor of four in a 22 bp target sequence. The frequency increases more than 13-fold in mutL and mutS host cells, suggesting that a high proportion of frameshift events are normally repaired by methyl-directed mismatch repair. Of the 87 sequenced frameshifts in this study, 96% result from deletion or insertion of only or two 2 bp repeat units. The most frequent events are 2 bp deletions, 2 bp insertions, and 4 bp deletions, the relative frequencies of these events being about 18:6:1.

Base Composition↗

Genotypic variation and stability of four variable-number tandem repeats and their suitability for discriminating strains of Mycobacterium leprae.

It has not been possible to distinguish different strains of Mycobacterium leprae according to their genetic sequence. However, the genome contains several variable-number tandem repeats (VNTR), which have been used effectively in strain typing of other bacteria. To determine their suitability for differentiating M. leprae, we developed PCR systems to amplify 5 different VNTR loci and examined a battery of 12 M. leprae strains derived from patients in different regions of the United States, Brazil, Mexico, and the Philippines, as well as from wild armadillos and a sooty mangabey monkey. We found diversity at four VNTR (D = 0.74), but one system (C(16)G(8)) failed to yield reproducible results. Alleles for the GAA VNTR varied in length from 10 to 16 copies, those for AT(17) varied in length from 10 to 15 copies, those for GTA varied in length from 9 to 12 copies, and those for TA(18) varied in length from 13 to 20 copies. Relatively little variation was seen with interspecies transfer of bacilli or during short-term passage of strains in nude mice or armadillos. The TA(18) locus was more polymorphic than other VNTR, and genotypic variation was more common after long-term expansion in armadillos. Most strain genotypes remained fairly stable in passage, but strain Thai-53 showed remarkable variability. Statistical cluster analysis segregated strains and passage samples appropriately but did not reveal any particular genotype associable with different regions or hosts of origin. VNTR polymorphisms can be used effectively to discriminate M. leprae strains. Inclusion of additional loci and other elements will likely lead to a robust typing system that can be used in community-based epidemiological studies and select clinical applications.

Genetic Variation↗

Differences and similarities between various tandem repeat sequences: minisatellites and microsatellites.

Tandemly repetitive DNA sequences are abundantly interspersed in the genome of practically all eukaryotic species studied. The relative occurrence of one type of repetitive sequence and its location in the genome appear to be species specific. A common property of repetitive sequences within the living world is their ability to give rise to variants with increased or reduced number of repeats. This instability depends upon numerous parameters whose exact role is unclear: the number of repeats, their sequence content, their chromosomal location, the mismatch repair capability of the cell, the developmental stage of the cell (mitotic or meiotic) and/or the sex of the transmitting parent. It is now apparent that mutations in repetitive sequences are a common cause of human disease, including cancer and disorders which may exhibit a dominant mode of inheritance. Two mechanisms have been proposed to explain the instability of repetitive sequences: DNA polymerase slippage, which may account for the instability of short repeats and unequal recombination which reshuffles repeat variants and maintains repeat heterogeneity in minisatellites. The purpose of this review is to show that no general rule can explain the instability of repetitive sequence. Each sequence of repeats is under the influence of local and general biological activities that determine its level of instability.

Animals↗

Periodicities and tandem repeats in a Balbiani ring gene.

The Balbiani ring (BR) DNAs show prominent periodicities of restriction enzyme sites. Studies using a cloned fragment of the BRc gene strongly suggest that these periodicities reflect the existence of tandemly repetitive sequences within BR DNA. Tandem repeats measuring 54-58 bp have been demonstrated by partial sequence analysis of the BRc clone; the restriction site periodicities suggest the existence of additional 175 (= 3 X 58) and 1050 (= 6 X 175) bp repeat units. The short, medium and long repeats (58, 175 and 1050 bp, respectively) show sequence homology. Constrained unequal crossing over (resulting from misalignment of repeat arrays, usually by one repeat) is proposed as the mechanism for evolution of short, medium and long repeats from each other, in a manner analogous to evolution of satellite DNA sequences. Paradoxically, the dominant restriction site periodicities appear to be more conservative than might be expected on the basis of the overall sequence divergence between the sequenced repeats. This may be a consequence of functionally important, long-range amino acid or oligopeptide periodicities (for example, Asp x Ser or Glu x Ser corresponding to Hinf I sites) in the BRc protein product, in conjunction with preferential use of certain synonymous codons.

Animals↗

Susceptibility to human type 1 diabetes at IDDM2 is determined by tandem repeat variation at the insulin gene minisatellite locus.

The IDDM2 locus encoding susceptibility to type 1 diabetes was mapped previously to a 4.1-kb region spanning the insulin gene and a minisatellite or variable number of tandem repeats (VNTR) locus on human chromosome 11p15.5. By 'cross-match' haplotype analysis and linkage disequilibrium mapping, we have mapped the mutation IDDM2 to within the VNTR itself. Other polymorphisms were systematically excluded as primary disease determinants. Transmission of IDDM2 may be influenced by parent-of-origin phenomena. Although we show that the insulin gene is expressed biallelically in the adult pancreas, we present preliminary evidence that the level of transcription in vivo is correlated with allelic variation within the VNTR. Allelic variation at VNTRs may play an important general role in human disease.

Adult↗

Rapid typing of tandemly repeated hypervariable loci by the polymerase chain reaction: application to the apolipoprotein B 3' hypervariable region.

The 3' flanking region of the apolipoprotein B (apoB) gene contains a hypervariable region consisting of a variable number of tandemly repeated short A + T-rich DNA sequences (VNTRs). We present a general method that utilizes the polymerase chain reaction to rapidly and accurately type this and other VNTR loci. We use tailored oligonucleotides and thermostable Taq polymerase to amplify the targeted region. The amplification products are directly visualized after agarose gel electrophoresis. Twelve alleles were readily identified in a sample of 125 unrelated individuals. The alleles differ with respect to the length of the amplified gene region. This genetic variability is inherited in an autosomal codominant manner. DNA sequence data indicate that individual alleles differ in the number of repeat units and the sensitivity of the technique is such that alleles differing in length by only 32 base pairs are readily distinguishable. A system of nomenclature based on the number of repeat units is suggested; an allele containing 37 repeat units is designated 3' beta 37, one containing 35 units is 3' beta 35, and so on. The frequency distribution of the 12 apoB VNTR alleles is bimodal with peaks at 37 and 47 repeat units and a nadir near 43 repeat units. We estimate that the 3' apoB VNTR locus has a heterozygosity index of 0.75 and a polymorphic information content of 0.73. It is a highly informative marker for genetic linkage studies on chromosome 2 and clinical and epidemiological studies involving the apoB gene. The high sensitivity and inexpensive nature of this technique make it superior to traditional Southern blot analysis for typing the 3' apoB VNTR. The method described is also directly applicable for rapid typing of other VNTRs in the human genome.

Alleles↗

Rapid and accurate characterisation of short tandem repeats by MALDI-TOF analysis of endonuclease cleaved RNA transcripts.

We describe the application of matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF MS) for the characterisation of short tandem repeat (STR) sequences by the analysis of endonuclease cleaved RNA transcripts. Several simple bovine STR loci as well as interrupted and compound microsatellites were chosen as model loci to evaluate the capabilities of MALDI-TOF MS for STR analysis. In short, the described approach consists of a PCR amplification of the investigated STR sequence, which then is transcribed into RNA and cleaved by G-specific RNase T1. Base-specific cleavage of the transcript results in high informative fragment patterns from both the repetitive core sequence and the flanking region. Since sequence specificity from endonuclease cleavage is combined with the accuracy of MALDI-TOF measurements, this technique allows for fast and reliable determination of simple repeat lengths as well as for further characterisation of STR allele sequences, which is of high interest especially in more complex STR loci.

Dinucleotide Repeats↗

Genotyping energy-transfer-cassette-labeled short-tandem-repeat amplicons with capillary array electrophoresis microchannel plates.

BACKGROUND: Genetic analysis of microsatellite DNA is a powerful tool used in linkage analysis, gene mapping, and clinical diagnosis. To address the expanding needs of studies of short tandem repeats (STRs), we demonstrated high-performance STR analysis on a high-throughput microchannel plate-based platform. METHODS: Energy-transfer-cassette-labeled STR amplicons were separated and typed on a microfabricated 96-channel radial capillary array electrophoresis (CAE) microchannel plate system. Four-color detection was accomplished with a laser-excited confocal fluorescence rotary scanner. RESULTS: Multiplex STR analysis with single base-pair resolution was demonstrated on denaturing polyacrylamide gel media. The high-throughput multiplex capabilities of this genetic analysis platform were demonstrated by the simultaneous separation of STR amplicons representing 122 samples in ninety-six 5.5-cm-long channels in <8 min. Sizing values obtained for these amplicons on the CAE microchannel plate were comparable to those measured on a conventional commercial CAE instrument and exhibit <1% sizing variance. CONCLUSIONS: Energy-transfer-cassette labeling and microfabricated CAE microchannel plates allow high-performance multiplex STR analyses.

Cell Line↗

Is the notch locus of Drosophila melanogaster a tandem repeat? Correlation of the genetic map and complementation pattern of selected mutations.

Correlation of the complementation relationships between the Notch locus alleles fa(g), fa(no), Ax(59d) and nd, with their genetic map order, suggests a tandem repetition within the locus of functionally related sites. This observation is discussed in relation to two hypotheses: (1) that the Notch locus contains a tandem repeat of genetic material; and (2) that the tertiary structure of the Notch locus product has a spiral configuration.

Alleles↗

Worldwide genetic relationships among Francisella tularensis isolates determined by multiple-locus variable-number tandem repeat analysis.

The intracellular bacterium Francisella tularensis is the causative agent of tularemia and poses a serious threat as an agent of bioterrorism. We have developed a highly effective molecular subtyping system from 25 variable-number tandem repeat (VNTR) loci. In our study, multiple-locus VNTR analysis (MLVA) was used to analyze genetic relationships and potential population structure within a global collection of 192 F. tularensis isolates, including representatives from each of the four subspecies. The VNTR loci displayed between 2 and 31 alleles with Nei's diversity values between 0.05 and 0.95. Neighbor-joining cluster analysis of VNTR data revealed 120 genotypes among the 192 F. tularensis isolates, including accurate subspecies identification. F. tularensis subsp. tularensis (type A) isolates showed great diversity at VNTR loci, while F. tularensis subsp. holarctica (type B) isolates showed much lower levels despite a much broader geographical prevalence. The resolution of two distinct clades within F. tularensis subsp. tularensis (designated A.I and A.II) revealed a previously unrecognized genetic division within this highly virulent subspecies. F. tularensis subsp. holarctica appears to have recently spread globally across continents from a single origin, while F. tularensis subsp. tularensis has a long and complex evolutionary history almost exclusively in North America. The sole non-North American type A isolates (Slovakian) were closely related to the SCHU S4 strain. Significant linkage disequilibrium was detected among VNTR loci of F. tularensis consistent with a clonal population structure. Overall, this work greatly augments the study of tularemia ecology and epidemiology, while providing a framework for future forensic analysis of F. tularensis isolates.

Alleles↗

Analysis of a variable number of tandem repeats in a heart disease gene by capillary electrophoresis with laser-induced fluorescence detector.

Capillary electrophoresis with laser-induced fluorescence detector (CE-LIF) was successfully applied to the analysis of the variable number of tandem repeats (VNTR) in a human apolipoprotein B gene (APOB). Apolipoprotein B VNTR alleles containing more than 35 repeat units are a significant risk factor for heart disease. Thus, we developed a method for accurately determining the number of repeat units (16 bp) in the VNTR using capillary electrophoresis. The CE-LIF technique gave excellent resolution of APOB alleles differing by 2 or 4 repeat units over the range 600 to 1000 bp. The recommended conditions for the analysis of APOB VNTR loci by CE-LIF are as follows: effective length of capillary (100 microns i.d., 360 microns o.d.), 50 cm; running buffer, 50 mM Tris-borate 0.5% methylcellulose and 0.1 microM fluorescent dye YO-PRO-1; electric field, 150 V/cm.

Alleles↗

[Polymorphisms of five short tandem repeat systems in Chinese Han population in Chengdu]

OBJECTIVE: To get preliminary genotype and allele frequency distributions of D6S366, D6S477, D12S375, D12S391 and PLA2A loci in Chinese Han population in Chengdu area and to validate more short Tandem repeat (STR) systems for forensic application. METHODS: The polymerase chain reaction (PCR) was used. Five STR systems (D6S366, D6S477, D12S375, D12S391 and PLA2A) were amplified on DNA samples, which were extracted from 108 unrelated individuals EDTA-blood by Phenol/Chloroform method. The PCR products were analyzed by PAG vertical electrophoresis. RESULTS: Seven alleles were found at D6S366 locus, nine alleles at D6S477 locus, five alleles at D12S375 locus, nine alleles at D12S391 locus and seven alleles at PLA2A locus. No deviations from Hardy-Weinberg equilibrium were observed. The heterozygosities observed were 0.69, 0.78, 0.81, 0.68 and 0.79 for D6S366, D6S477, D12S375, D12S391 and PLA2A respectively. The chances of exclusion were 0.3621, 0.6004, 0.4581, 0.7014 and 0.5589 and the discriminating powers were 0.79, 0.93, 0.86, 0.96 and 0.91. CONCLUSION: All of the five loci in this study were useful markers for individual identification and paternity test and for genetics purposes.

Journal Article↗

Short tandem repeat typing of bodies from a mass disaster: high success rate and characteristic amplification patterns in highly degraded samples.

We have used a PCR-based DNA-typing method, involving the coamplification of four tetrameric short tandem repeat loci, in the analysis of a large number of severely degraded tissue samples taken from the scene of a mass disaster in which bodies were exposed to extreme thermal, physical and chemical insult. Analysis of the amplified DNA in a number of the samples revealed uniquely sized artifact PCR products resulting from the amplification of degraded genomic DNA as well as characteristic patterns in the amounts of PCR products generated from differently sized loci. This system has proved to be very reliable and robust, and we were successful in typing all of the four loci in 66% of the samples tested and at least one locus in 83% of the cases. A PCR-based sex test also proved to be very effective when applied to the degraded samples.

Alleles↗

The ribosomal RNA gene region of Nosema apis (Microspora): DNA sequence for small and large subunit rRNA genes and evidence of a large tandem repeat unit size.

The ribosomal RNA (rRNA) gene region of the microsporidium, Nosema apis, has been examined. A new method for extracting microsporidian genomic DNA from infected host tissue is described. Complete DNA sequence data are presented for the small subunit gene (1242 bp), the internal transcribed space (33 bp), and the large subunit gene (2481 bp to a putative termination point). This is the first time that the complete large subunit rRNA gene has been published for any microsporidian species. DNA sequence is also presented for the regions flanking the 5' end of the small subunit gene and the 3' end of the large subunit gene. The intergenic spacer is shown to be heterogeneous, showing variation in sequence and restriction sites rather than length and containing sequence repeats, which are a characteristic feature of intergenic spacers. The rRNA gene region of N. apis is shown to occur in a head-to-tail, tandemly repeated manner, as in other eukaryotes. This repeat unit is shown to be approximately 18 kb in length. The nucleotide sequence presented has been submitted to the Genbank database under the accession number U97150.

Animals↗

Intra- and inter-population diversity at short tandem repeat loci in diverse populations of the world.

To study the level of intra- and inter-population variation at hypervariable DNA loci, we have characterized 15 human populations of diverse ethnic and geographic origins at six short tandem repeat loci by using the polymerase chain reaction. Even though the spectrum of allelic variation is quite broad and there are substantial differences in allele frequency distributions among populations, in general, population within a major racial group show a greater degree of similarity. This observation is reflected in the analysis of gene diversity. When the total diversity is apportioned, the maximum variation becomes attributable to inter-individual differences within a population; of the variation that is attributed to differences between populations within a racial group and differences between racial groups, namely, African, Caucasian, and Mongoloid, than the American Indians and the Pacific Islanders. As expected, a reciprocal relationship between gene diversity and FST levels is observed. Higher values of FST in the American Indian and the Pacific Islanders may reflect smaller population size and a higher level of isolation. An analysis of genetic distance encompassing the populations belonging to the three major racial groups recognizes three distinct clusters - all the populations of African affiliation cluster together, as do the Caucasian affiliated and the Mongoloid groups, in two distinct clusters. Interestingly, three broadly classified cosmopolitan US populations, namely, US White, US Black and US Asian, cluster with their ancestrally related populations. This study dispels some of the concerns regarding the applicability of DNA typing data for forensic use.

Alleles↗

PCR analysis of the short tandem repeat (STR) system HUMVWA31. Allele and genotype frequencies in an Italian population sample.

A population study in a sample of 211 unrelated individuals from 2 cities in North and Central Italy was carried out to investigate the short tandem repeat (STR) system HUMVWA31. Separation of PCR- amplified DNA fragments was performed by high-resolution horizontal denaturing polyacrylamide gel electrophoresis (PAGE) followed by silver staining. The 7 common alleles were found, together with a new smaller allele. Distribution of the observed genotypes did not deviate from Hardy-Weinberg (H-W) equilibrium. The power of discrimination for this locus was 0.93 and the chance of exclusion was 0.61. Good agreement was found between the allele frequencies in 2 Italian population samples and previous studies on Caucasians. The results of this study suggest that this STR system may be a useful tool in forensic investigations.

Alleles↗

The RNA polymerase I transcription factor xUBF contains 5 tandemly repeated HMG homology boxes.

The RNA polymerase I transcription factor UBF has been identified in human, mouse, rat and Xenopus and the primary structure of the human protein has been determined. Human UBF was shown to contain four tandem homologies to the folding domains of the HMG1 and 2 proteins and hence to belong to a previously unrecognised family of 'HMG-box' transcription factors. Here, cDNA clones encoding the Xenopus laevis UBF (xUBF) have been isolated and sequenced. Northern and Southern blots revealed that in tissue culture cells, xUBF is coded on a single major mRNA size species by a small number of genes. The deduced primary structure of xUBF is highly homologous with the human protein except for a central deletion which removes most of one HMG-box. This explains the major size difference between the X. laevis and human proteins and may well explain their different transcriptional specificities. It is shown that xUBF contains 5 tandemly repeated HMG-boxes and that by analogy the human protein contains 6.

Amino Acid Sequence↗