Bacterial Typing Techniques ; Genotype ; Minisatellite Repeats ; Plague ; Yersinia pestis ; genetics

Collaborative work using same samples for the parentage testing, which was intended to see the status and the quality of several DNA typing laboratories in Korea, was described. Samples were consisted of two sets, one was a trio case and the other was a deficient case with two children. Samples were sent to six laboratories, among which five submitted the result. Each laboratory had used different number and set of STR loci using 14 - 23 loci, and total 33 different loci were used. Only one VNTR locus, D1S80 was included and all the remaining were STR loci. The loci included in the commercial kits were used more frequently. One laboratory had used Korean-made commercial kits. All the laboratories gave the same results about the parentage, although results for one locus were not the same through different laboratories. There existed minor difference in the PI calculation, especially in the statistical parameters such as allelic frequences, which might gave confusion to users of the results who were not familiar with the test. Necessity about the standardization and profiling data were discussed.
Academies and Institutes* ; Child ; DNA Fingerprinting ; Humans ; Korea* ; Minisatellite Repeats

OBJECTIVEHuman Lyme Borreliosis (LB), which is caused by Borrelia burgdorferi sensu lato (B. burgdorferi), has been identified as a major arthropod-borne infectious disease in China. We aimed to develop a multiple locus variable-number tandem repeat (VNTR) analysis (MLVA) assay for the genotyping of Borrelia burgdorferi strains detected in China.

METHODSB. garinii PBi complete 904.246 kb chromosome and two plasmids (cp26 and lp54) were screened by using Tandem Repeats Finder program for getting potential VNTR loci, the potential VNTR loci were analyzed and identified with PCR and the VNTR loci data were analyzed and MLVA clustering tree were constrcted by using the categorical coefficient and the unweighted pair-group method with arithmetic means (UPGMA).

RESULTSWe identified 5 new VNTR loci through analyzing 47 potential VNTR loci. We used the MLVA protocol to analyse 101 B. burgdorferi strains detected in China and finally identified 51 unique genotypes in 4 major clusters including B. burgdorferi sensu stricto (B.b.s.s), B. garinii, B. afzelii, and B. valaisiana, consistent with the current MLSA phylogeny studies. The allele numbers of VNTR-1, VNTR-2, VNTR-3, VNTR-4, and VNTR-5 were 7, 3, 9, 7, and 6. The Hunter-Gaston index (HGI) of five VNTR loci were 0.79, 0.22, 0.77, 0.71, and 0.67, respectively. The combined HGI of five VNTR loci was 0.96. Clustering of the strains of Xinjiang, Inner Mongolia and Heilongjiang was confirmed, and this situation was consistent with the close geographical distribution of those provinces.

CONCLUSIONThe MLVA protocol esytablished in this study is easy and can show strains' phylogenetic relationships to distinguish the strains of Borrelia species. It is useful for further phylogenetic and epidemiological analyses of Borrelia strains.

No abstract available.
DNA Fingerprinting* ; DNA* ; Family Relations* ; Humans ; Minisatellite Repeats*

To know the amplification pattern according to relative concentration ratio in mixed samples, two STRloci, vwF locus and MBP locus and two VNTR loci, D1S80 locus and d17S5 locus were amplified in DNA with various concentration of two individuals were easily identified. But when the concentration of one person were lowered to 1/20-1/40 of the other's the intensity of product bands diminshed and hardly discernible. Also different amplification efficiency according to the template length was noted, especially in VNTR loci. Using automatic sequencer and RFLP scan program, the intensity OD of each PCR product band could be calculated, and this correlates the felative amplification efficiency of each allele. By using this we could construct quantitative PCR for the mixed samples. This could be used in practical case work for forensic purpose, and also be a valuable candidate for 'chimerism detection' in case of bone marrow transplatation.
Alleles ; Bone Marrow ; DNA ; Humans ; Minisatellite Repeats ; Polymerase Chain Reaction* ; Polymorphism, Restriction Fragment Length

OBJECTIVETo evaluate four candidate variable number tandem repeat (VNTR) loci for genotyping Mycobacterium tuberculosis complex strains.

METHODSGenomic sequences for two M. tuberculosis strains (CCDC5079 and CCDC5180) were generated, and using published sequence data, four candidate VNTR loci were identified. The VNTRs were used to genotype 225 Chinese clinical M. tuberculosis complex strains. The discriminatory power of the VNTRs was evaluated using BioNumerics 5.0 software.

RESULTSThe Hunter-Gaston Index (HGI) for BJ1, BJ2, BJ3, and BJ4 loci was 0.634, 0.917, 0.697, and 0.910, respectively. Combining all four loci gave an HGI value of 0.995, thus confirming that the genotyping had good discriminatory power. The HGI values for BJ1, BJ2, BJ3, and BJ4, obtained from Beijing family strain genotyping, were 0.447, 0.878, 0.315, and 0.850, respectively. Combining all four loci produced an HGI value of 0.988 for genotyping the Beijing family strains. We observed unique patterns for M. bovis and M. africanum strains from the four loci.

CONCLUSIONWe have shown that the four VNTR loci can be successfully used for genotyping M. tuberculosis complex strains. Notably, these new loci may provide additional information about Chinese M. tuberculosis isolates than that currently afforded by established VNTR loci typing.

OBJECTIVETo develop a multiple-locus variable-number tandem-repeat (VNTR) analysis (MLVA) assay for Acinetobacter pittii typing.

METHODSPolymorphic VNTRs were searched by Tandem Repeats Finder. The distribution and polymorphism of each VNTR locus were analyzed in all the A. pittii genomes deposited in the NCBI genome database by BLAST and were evaluated with a collection of 20 well-characterized clinical A. pittii strains and one reference strain. The MLVA assay was compared with pulsed-field gel electrophoresis (PFGE) for discriminating A. pittii isolates.

RESULTSTen VNTR loci were identified upon bioinformatic screening of A. pittii genomes, but only five of them showed full amplifiability and good polymorphism. Therefore, an MLVA assay composed of five VNTR loci was developed. The typeability, reproducibility, stability, discriminatory power, and epidemiological concordance were excellent. Compared with PFGE, the new optimized MLVA typing scheme provided the same and even greater discrimination.

CONCLUSIONCompared with PFGE, MLVA typing is a faster and more standardized alternative for studying the genetic relatedness of A. pittii isolates in disease surveillance and outbreak investigation.

Bacterial Typing Techniques ; Leptospira interrogans ; classification ; genetics ; Minisatellite Repeats ; Multilocus Sequence Typing ; methods

OBJECTIVETo study the expression of Aggrecan and the relationship between the variable number of tandem repeats (VNTR) of Aggrecan and lumbar disc herniation (LDH).

METHODSThe disease group comprised of 74 patients already diagnosed with symptomatic LDH. The control group consisted of 15 patients restricted to spinal trauma and 113 healthy blood donors without symptoms of LDH who were not diagnosed with LDH. Disc tissue samples were obtained from surgical operations and blood samples were donated from all participants. The Aggrecan expression in isolated tissues was assessed by western blot using specific antibodies. The Aggrecan gene VNTR region was analyzed by PCR.

RESULTSThe Aggrecan expression positive rate of control group was statistically and significantly higher (control group:86.67%, disease group:13.51%;χ(2) = 34.83, P < 0.05) than that of the disease group. Moreover, there was a statistically significant higher frequency of Allele 25 or Allele 21 in disease group compared to controls (A25disease group = 22.97%, A25control group = 12.11%, χ(2)A25 = 8.20, PA25 = 0.004; A21disease group = 6.76%, A21control group = 0.39%, χ(2)A21 = 14.35, PA21 = 0.000). Compared to the participants with 2 Alleles>25 repeats, subjects with 1 or 2 Alleles ≤ 25 repeats statistically and significantly over represented the disease group without the expression of Aggrecan (χ(2) = 5.69, P = 0.017).

CONCLUSIONSThe findings suggest a relationship between Aggrecan and symptomatic LDH, where symptomatic LDH has a tendency of allele 21 and allele 25 repeats.In addition, an association between the distribution of Aggrecan gene VNTR polymorphism and the expression of Aggrecan is observed in symptomatic LDH.

Animals ; Genotype ; Humans ; Leptospira interrogans ; classification ; genetics ; Minisatellite Repeats ; genetics ; Molecular Epidemiology ; methods