OBJECTIVETo analyze the rare alleles of D13S325 locus which fell in the size range of D12S391 locus with the STRtyper-10G kit.

METHODSGenotyping results of cases with suspected rare alleles of D13S325 were verified with Sinofiler(TM) kit and a singleplex amplification system. The rare alleles were separated and sequenced.

RESULTSFive families were detected with rare alleles of the D13S325 locus, which were misread as allele 20 of D12S391 locus. The alleles were named as 5.1 based on DNA sequences and have a frequency of 0.156 × 10(-2).

CONCLUSIONAs the rare allele 5.1 of D13S325 locus with the STRtyper-10G kit is prone to be mistyped, attention should be paid in the paternity testing, personal identification and DNA database search.

Alleles ; Humans ; Paternity ; Tandem Repeat Sequences

OBJECTIVETo understand the allele structure and genetic polymorphism at D3S1358, D13S317, D5S818 short tandem repeats (STRs) loci in Nongqu Mongolian of China, and to construct a preliminary database.

METHODSThe allele frequencies of the three STRs loci in 291 unrelated individuals from Nongqu Mongolian were analyzed by polymerase chain reaction and polyacrylamide gel electrophoresis.

RESULTSSix, ten, and eight alleles were observed at D3S1358, D13S317, D5S818, respectively, and all 3 loci met Hardy-Weinberg equilibrium. The statistical analysis of 3 STR loci showed the heterozygosity >or=0.7332, the polymorphic information content >or=0.6884; the combined discrimination power and the probabilities of paternity exclusion were 0.9991 and 0.9806 respectively.

CONCLUSIONAll three of the loci in this study were found to have high heterozygosity and polymorphic information content, so they could provide useful markers for genetic purposes. These results could serve as valuable data to enrich the Mongolian genetic database and play an important role in Chinese population genetic application.

Chromosome Mapping ; Humans ; Mongolia ; ethnology ; Polymorphism, Genetic ; Tandem Repeat Sequences

OBJECTIVETo know the genotype and allele frequency distribution of D1S549, D3S1754 and D12S375 in Chinese Han population in the Qingdao area and to study the three short tandem repeat(STR) loci for genetic application.

METHODSACD-blood specimens were collected from the unrelated individuals in Qingdao. The DNA samples were extracted with the use of Chelex method and were amplified by polymerase chain reaction (PCR) technique. The PCR products were analyzed by polyacrylamide gel electrophoresis and were visualized by silver staining.

RESULTSEight alleles were found at D1S549 locus, eight alleles at D3S1754 locus and five alleles at D12S375 locus, and 22, 19 and 14 genotypes were identified respectively. No deviation from Hardy-Weinberg equilibrium was observed in the three loci. The heterozygosities expected of them were 0.7988, 0.7087 and 0.75 respectively. The exclusion probability was calculated as 0.6592 for D1S549, and 0.5605 for D3S1754, and 0.5864 for D12S375. The discriminating power of the three loci were 0.9143, 0.8382 and 0.8861. Comparison of the allelic frequencies in Qingdao area with those in Hans of Chengdu area by chi-square test showed a difference statistically significant at D1S549 locus but no difference at D3S1754 and D12S375 loci.

CONCLUSIONThis study reveals the structure of the three loci and the obtained data are beneficial to understanding the population genetics in Chinese Han population. All of the three loci have higher chance of exclusion and higher discriminating power, and they will be useful markers for individual identification, paternity test and genetics purposes.

China ; ethnology ; Gene Frequency ; Humans ; Polymorphism, Genetic ; Tandem Repeat Sequences

OBJECTIVETo study genetic polymorphism of 9 STR loci in Han nation population in Shangdong Province.

METHODSWe investigated 100 unrelated individuals of Han nation population in Shandong Province and studied their genetic distribution of 9 STR loci and Amelogenin locus. Primers of 10 loci were labeled with the NHS-ester fluorescent dye 5-FAM (blue), Joe (green) or NED (yellow). The data of Han nation population were generated by multiple amplification and subjected to GeneScan, genotype and genetic distribution analysis.

RESULTS83 alleles and 220 genotypes were observed, with the corresponding frequency of 0.0050-0.4050 and 0.0100-0.2100. The average of heterozygosity was 0.7778, the accumulated discrimination power was 0.9999. The accumulated probability of exclusion paternity was 0.9999. The polymorphism information content was 0.5823-0.8396.

CONCLUSIONSChi-Square test indicated that the distribution of genotypes agreed with Hardy-Weinberg equilibrium.

Alleles ; China ; ethnology ; Gene Frequency ; Genetic Markers ; genetics ; Genotype ; Humans ; Polymorphism, Genetic ; Repetitive Sequences, Nucleic Acid ; Tandem Repeat Sequences

We compared genetic variations in virulence mega plasmids pXO1 and pXO2 of twenty-seven Bacillus anthracis strains from Korean patients and environmental samples together with those of Bacillus anthracis Sterne, Pasteur and A2012 standard strains. Genetic variations were analyzed in twenty-three variable regions (ten and thirteen variablenumber tandem repeats and insertion/deletions in pXO1 and pXO2, respectively). The pXO1 plasmids were classified into 7 groups and pXO2 plasmids to 12 groups. Discrete phylogenic lineages could be differentiated between environmental and clinical strains by UPGMA (unweighted pair group method with average) method. In addition, clinical strains showed more variations than environmental isolates. The pXO2 plasmid appeared genetically more unstable than pXO1. A general plasmid genotype could be suggested for Korean soil isolates since they mostly clustered into a representative group.
Bacillus anthracis* ; Bacillus* ; Genetic Variation* ; Genotype ; Humans ; Korea* ; Plasmids* ; Soil ; Tandem Repeat Sequences ; Virulence

PURPOSE: Telomeres, special protein and tandem repeat DNA structure that cap the ends of linear eukaryotic chromosomes, are essential for chromosome structure and stability. Human telomeric DNA is known to shorten by 30~200 bp with each somatic cell division. However, the phase of telomere changes has not been studied extensively. METHODS: Telomere length was analyzed in the peripheral blood mononuclear cells (PBMCs) of 39 normal controls aged from newborn to 72 years by Southern blot hybridization using PharMingen's TeloQunatTM Telomere Length Assay Kit (Becton Dickinson Co.). RESULTS: The mean telomere length of the population was 9.68 kb (range, 5.65~14.40 kb). The length (kb) decreased with age (A) by the following regression: T=10.86 0.04 A (T=telomere length in kb; A=age in years) (r= 0.38; P=0.016). The mean telomere lengths according to age groups were: 10.26 kb for less than 15 years; 9.92 kb for 16 to 40 years; 8.03 kb for over 40 years. The telomere length of over 40 years was significantly shorter than that of less than 15 years (P=0.013), and than that of 16 to 40 years (P=0.011). The phase of telomere changes was evaluated by age subgroups. The shortening was fastest in individuals of age <5, while the length showed a plateau or slight increment in age group between 5 to 35. The length decreased steadily with age by the regression of 12.43+/-0.07 A (r= 0.500; P=0.034) in age group over 35. CONCLUSION: Telomere length of PBMCs decreases with age, and the different phase of telomere length shortening may suggest that the shortening of telomere is not a constant process over lifespan, but a dynamic process that is differently regulated in age groups.
Blotting, Southern ; Cell Division ; Chromosome Structures ; DNA ; Humans ; Infant, Newborn ; Tandem Repeat Sequences ; Telomere Shortening* ; Telomere*

OBJECTIVETo investigate the distribution of CSF1PO, TPOX and TH01 in 5 minority populations only resided in Yunnan province.

METHODSDNA extraction from bloods and multiplex amplification of CSF1PO, TPOX and TH01 were carried out. The technique of denaturing polyacrylamide gel electrophoresis and silver staining method were used.

RESULTSThe data on the distribution of allele frequencies of 3 loci(CSF1PO, TPOX and TH01) in Achang Deang Bulang Pumi and Jino were collected and analyzed.

CONCLUSIONThe allele distribution of the loci were in good agreement with the Hardy-Weinberg equibrium. A satisfactory result was obtained and some significant genetics differences were noticed in different populations.

Alleles ; China ; Female ; Gene Frequency ; Genotype ; Humans ; Male ; Tandem Repeat Sequences ; genetics

Tandem-repeated sequence of nucleic acid was constructed by splicing 4 fragments which contain the same sequence in the central part, using overlap extension polymerase chain reaction and then repeatedly cloning it in the same vector at different site of restriction endonuclease. Its signal amplification action was evaluated using electrophoresis of hybridized product and dot hybridization assay. 24-repeat sequence was successfully constructed and confirmed by restriction endonuclease digestion analysis. The construct was 25-repeat actually since the vector itself had the same basic sequence. Hybridized product electrophoresis revealed that the 25-repeat sequence could combine with several secondary probes. Dot hybridization assay demonstrated that tandem-repeated sequence was 16-fold more sensitive than that of non-repeated sequence. Tandem-repeated sequence had good effect on signal amplification. It could be easily cheaply prepared in large amount after cloning. Thus, it might be useful in clinical examinations and biological researches.
Genetic Vectors ; Nucleic Acid Hybridization ; methods ; Polymerase Chain Reaction ; methods ; Tandem Repeat Sequences ; genetics

As a protein originally found in plant pathogenic bacteria, transcription activator-like effectors (TALEs) can be fused with the cleaving domain of restriction endonuclease (For example Fok I) to form artificial nucleases named TALENs. These proteins are dependent on variable numbers of tandem Repeats of TALEs to recognize and bind DNA sequences. Each of these repeats consists of a set of approximately 34 amino acids, composed of about 32 conserved amino acids and 2 highly variable amino acids called repeat variant di-residues (RVDs). RVDs distinguish one TALE from another and can make TALEs have a simple cipher for the one-to-one recognition for proteins and DNA bases. Based on this, in theory, artificially constructed TALENs could recognize and break DNA sites specifically and arbitrarily to perform gene knockout, insertion or modification. We reviewed the development of this technology in multi-level and multi species, and its advantages and disadvantages compared with ZFNs and CRISPR/Cas technology. We also address its special advantages in industrial microbe breeding, vector construction, targeting precision, high efficiency of editing and biological safety.
Amino Acid Motifs ; Biotechnology ; DNA ; chemistry ; Endonucleases ; chemistry ; Tandem Repeat Sequences ; Trans-Activators ; chemistry

OBJECTIVETo review the common genotyping techniques of Chlamydia trachomatis in terms of their principles, characteristics, applications and limitations.

DATA SOURCESData used in this review were mainly from English literatures of PubMed database. The search terms were "Chlamydia trachomatis" and "genotyping". Meanwhile, data from World Health Organization were also cited.

STUDY SELECTIONOriginal articles and reviews relevant to present review's theme were selected.

RESULTSDifferent genotyping techniques were applied on different occasions according to their characteristics, especially in epidemiological studies worldwide, which pushed the study of Chlamydia trachomatis forward greatly. In addition, summaries of some epidemiological studies by genotyping were also included in this work for reference and comparison.

CONCLUSIONSA clear understanding of common genotyping techniques could be helpful to genotype C. trachomatis more appropriately and effectively. Furthermore, more studies on the association of genotypes of Chlamydia trachomatis with clinical manifestations should be performed.

Chlamydia trachomatis ; genetics ; Genotype ; Multilocus Sequence Typing ; Polymerase Chain Reaction ; Tandem Repeat Sequences ; genetics