There are several methods for diagnosis of leprosy, including AFB stain, the measurement of PGL-1 (phenolic glycolipid - 1) antigen titer, and DNA-PCR. In this study, we have used the DNA-PCR amplifying the RLEP repetitive sequence. Our result showed that the RLEP primer offered the more sensitive detection and identification of M. leprae DNA in clinical specimens, compared with the other primer, for example, 18-kDa antigen gene. To screen the resistant M. leprae strain of MDT (Multi-Drug Therapy), we have used the TD (Touch-Down) PCR. We arranged and amplified sequences of the genes, folP, rpoB, gyr, 23S rRNA, in M. leprae involved in MDT-resistance, and could obtain the PCR product each gene, simultaneously. This method, based on annealing temperature, was useful to the detection for diagnosis and the screen of MDT-resistant strain of M. leprae, rapidly. Thus, we suggest that the RLEP primer and TD-PCR method are effective in assessing the diagnosis of leprosy and the identification of drug-resistant M. leprae.
Diagnosis* ; DNA ; Leprosy* ; Polymerase Chain Reaction* ; Repetitive Sequences, Nucleic Acid

Repetitive sequences such as SINE, LINE, and LTR elements form a major part of eukaryotic genomes. A literature search tool that summarizes the information contained within repeat elements would provide biologists in the field of genomics with a useful tool for analyzing genomic sequence features. We developed a java program designed to make literature access easier by using two search engines simultaneously. RepWeb is a web-based search system that provides a user friendly interface for searching the reference data and journals for information related to repeat elements by using the search engines, Google Scholar and PubMed, simultaneously. It provides an interface that displays the repeat element- related biological information, and includes useful functions such as the production of a repeat tree, clickable links to PubMed and Google Scholar, exporting, and sorting a field into date, author, journal and title.
Genome ; Genomics ; Indonesia ; Repetitive Sequences, Nucleic Acid ; Search Engine

In this study, the molecular marker technology of SRAP and ISSR were applied in rapid identification of seeds from eight species of Brassica oleracea L. Firstly, using the genomic DNA of cabbage as template, SRAP and ISSR reaction systems were optimized through testing every factor, respectively, that affects PCR amplification. Then, using the optimized reaction systems, 30 SRAP primer pairs and 15 ISSR primers were applied to amplify genomic DNA of cabbage, savoy, purple cabbage, borecole, cauliflower, broccoli, Brussels sprouts, and kohlrabi The results showed that high polymorphisms were exhibited among the eight species of Brassica oleracea L. by SRAP primer pairs of M3-E5 and M4-E5, as well as ISSR primers of 844 and 888, especially primer 844 which can identify all eight materials efficiently.
Brassica ; genetics ; Nucleic Acid Amplification Techniques ; methods ; Polymorphism, Genetic ; Repetitive Sequences, Nucleic Acid ; Seeds ; genetics

We determined the genetic diversity and distance between Jeju and Thoroughbred horses by genotyping for 20 microsatellite loci consisting of (TG)n repetitive sequence. The expected heterozygosity ranged from 0.1 to 0.789 in the Jeju horses and from 0.505 to 0.824 in the Thoroughbred horses. Polymorphic information content (PIC) values ranged from 0.09 to 0.709 in the Jeju horses and 0.365 to 0.730 in Thoroughbred horses. There were no significant differences in heterozygosity and PIC values between Jeju and Thoroughbred horsesHowever, LEX035 was estimated relatively high heterozygosity (0.789) and PIC value 0.709) in Jeju horses and LEX050 was respectively 0.824, and 0.730 in the Thoroughbred horses. We may conclude that the genetic differentiation was low between Jeju and Thoroughbred horses. LEX 050, LEX055, LEX059 and LEX 063 could be used as geneticmarkers for differentiating Jeju from Thoroughbred horses.
DNA ; Genetic Markers ; Genetic Variation ; Horses ; Korea ; Microsatellite Repeats ; Polymorphism, Genetic ; Repetitive Sequences, Nucleic Acid

BACKGROUND: Chicken pox and herpes zoster are caused by the varicella-zoster virus(VZV). To investigate the epiderniologial relationship between clinical isolates of VZV, it is essential to distinguish different isolate. OBJECTIVE: This study was conducted to classify the VZV strains according to R5 tandem direct reiterations(TDR) copy numbers and Pst I endonuclease cleavage site mutation, and to analyze the distribution pattern of VZV strains isolated in Korea. METHODS: Strains of VZV were isolated from 61 patients with herpes zoster who had not been immunized with a live vaccine of VZV. Copy numbers of R5 TDR which was located in variable region IV were measured by PCR. The presence of a Pst I cleavage site in a middle portion of the long unique region of VZV genome was analyzed by PCR thereafter restriction enzyme digestion(PCR-RFLP). RESULTS: VZV strains isolated in Korea contained one to three copy numbers of R5 TDR. Of 61 isolates, 43(70%) comtained 2 copies of R5 TDR, while 11(18%) isolates contained only one copy and 7(12%) isolat s contained 3 copies. About 16% of the strains examined did not have a PstI cleavage site, although the majority of strains retained this site. VZV strains could be classified into 6 strains on the basis of the copy number of R5 TDR and PstI cleavage site, in which the strain with 2 copies of R5 TDR and PstI cleavage site positive was the most frequent type (36 out of 61 isolates) in Korea. Four batches of live attenuated vaccine(Biken) that is now used in Korea showed 2 copy numbers of R5 TDR and PstI site negative. CONCLUSION: The copy number of R5 TDR and the presence of PstI cleavage site seems to be a reliable marker for dicrimination of VZV strains in Korea. This discrimination can be used to study the molecular epiclemiology of VZV and as a criterion for identification of vaccine-related isolates.
Chickenpox* ; Discrimination (Psychology) ; Genome ; Herpes Zoster* ; Humans ; Korea* ; Polymerase Chain Reaction ; Repetitive Sequences, Nucleic Acid*

In order to observe the changes in left ventricular systolic and diastolic function by repetitive regional myocardial ischemia and reperfusion, left anterior descending artery(LAD) just distal to the first diagonal branch in nine mongrel dogs was obstructed for 1 minute and reperfused for 15 minutes twice (first and second obstruction and reperfusion), and as a third trial repeated obstruction for 5 minutes and reperfusion for 15 minutes was done. Then the last obstruction for 1 minute and reperfusion for 15 mintues was performed. Peak positive dp/dt, left ventricular systolic pressure(LVSP) and systolic thickening were used as systolic parameters and peak negative dp/dt, left ventricular end diastolic pressure (LVEDP) and time constant of isovolumic relaxation were used as diastolic parameters. The results are as follows : 1) After first reperfusion, all systolic and diastolic parameters showed no significant changes except systolic thickening, which fell from the basal line(48.9+/-16.6% versus 59.8+/-10.0%, p<0.05). 2) After second reperfusion, peak positive dp/dt and systolic thickening decreased (1475+/-342mmHG/sec versus 1561+/-307mmHg/sec,p<0.05; 48.2+/-6.1% versus 59.8+/-10.05%, p<0.005 respectively). But LSVP, LVEDP, peak negative dp/dt and T showed no significant changes. 3) After third reperfusion all systolic and diastolic parameters except LVEDP showed significant impairment by 5 minutes of coronary occlusion, which means postischemic prolonged myocardial dysfunction(peak positive dp/dt 1401+/-362mmHg/sec versus 1561+/-307mmHg/sec, p<0.005; LVSP 88.5+/-23.4mmHg versus 97.6+/-25.4mmHg, p<0.05; systolic thickening 41.2+/-8.2% versus 59.8+/-10.0%, p<0.005; peak negative dp/dt -879+/-299mmHg/sec versus -1037+/-297mmHg/sec, p<0.05; T 46.3+/-8.2 msec versus 41.9+/-6.1 msec, p<0.01). 4) All observed systolic and diastolic parameters also revealed myocardial dysfunction after fourth reperfusion(peak positive dp/dt 1348+/-288mmHg/sec versus 1561+/-307mmHg/sec, p<0.0005; LVSP 88.5+/-24.1mmHg versus 97.6+/-25.4mmHg, p<0.005;systolic thickening 32.1+/-8.9 versus 59.8+/-10.0%, p<0.001; peak negative dp/dt -850+/-260mmHg/sec versus -1037+/-297mmHg, p<0.05; LVEDP 6.6+/-1.7mmHg versus 5.4+/-1.3mmHg, p<0.05; T 49.9+/-9.8msec versus 41.9+/-6.1msec, p<0.01). 5) Overall tendencies of myocardidal impairment were statistically significant in each parameter (peak positive dp/dt, p<0.001; systolic thickening, p<0.05; LVEDP, p<0.05; T, p<0.01) except LVSP and peak negative dp/dt. Thus myocardial function was impaired progressively by repetitive regional myocardial ischemia and reperfusion. In conclusion, a 5 minute coronary occlusion results in postischemic prolonged myocardial ischemia and repetitive coronary occlusion and reperfusion may show cumulative effect.
Animals ; Blood Pressure ; Coronary Occlusion ; Coronary Vessels* ; Dogs ; Myocardial Ischemia ; Relaxation ; Reperfusion* ; Repetitive Sequences, Nucleic Acid

Drought, flood, salinity, or a combination of these limits rice production. Several rice varieties are well known for their tolerance to specific abiotic stresses. We determined genetic relationship among 12 rice varieties including 9 tolerant to drought, flood, or salinity using inter-simple sequence repeat (ISSR) markers. Based on all markers, the nine tolerant varieties formed one cluster distinct from the cluster of three control varieties. The salt-tolerant varieties were closest to two flood-tolerant varieties, and together they were distinct from the drought-tolerant varieties. (GA)(8)YG was the most informative primer, showing the highest polymorphic information content (PIC) and resolving power (Rp). The drought-, flood-, and salt-tolerant varieties grouped in three distinct clusters within the group of tolerant varieties, when (GA)(8)YG was used. Sabita was the only exception. The two aus varieties, Nagina22 and FR13A, were separated and grouped with the drought- and flood-tolerant varieties, respectively, but they were together in dendrograms based on other primers. The results show that ISSR markers associated with (GA)(8)YG delineated the three groups of stress-tolerant varieties from each other and can be used to identify genes/new alleles associated with the three abiotic stresses in rice germplasm.
Droughts ; Floods ; Genotype ; Oryza ; classification ; genetics ; Repetitive Sequences, Nucleic Acid ; Salinity

OBJECTIVETo detect genetic diversity of 48 population of Polygonum capitatum in Guizhou province.

METHODThe genetic diversity of 48 representational populations of P. capitatum including 240 individuals had been investigated by ISSR marker technique.

RESULTThe genetic diversity had been revealed as follow: A total of 8 293 bands were produced in 240 individuals, of which 7 962 bands were common in the 48 population. The value of the average percentage of polymorphic bands (PPB) was 79.09%, Nei's genetic diversity index (H(e)) was 0.245 8, Shannon's information index (I) was 0.396 2, and genetic differentiation index (G(st)) was 0.238 0 at population level, respectively. The genetic differentiation index (G(st)) was 0.072 2, genetic differentiation coefficient by Shannon's diversity (I(st)) was 0.044 2 within the population levels. Groups cluster analysis based on the UPGMA method indicated that although the 48 populations could be divided into 3 groups and the P. capitatum seed sources. The groups cluster showed that a cross clustering of P. capitatum between the southwest and southeast populations in Guizhou province, and no significant correlation was found between geographical and genetic distance among them.

CONCLUSIONThe genetic diversity of P. capitatum is relatively high at the population levels, while low within the population levels, a significant degree of genetic differentiation occurs among the populations. The groups cluster analysis indicated they has not apparent genetic variation in regional pattern between the place of origin populations and the migrate populations.

This article assessed the genetic relationship and genetic diversity in Dioscorea alata. Twenty samples were examined to identify their original plants, and analyzed by ISSR markers. The results showed that 20 samples were classified into three different plants, such as D. alata, D. persimilis, and D. fordii. There was significant difference in genetic similarity coefficient between D. alata and D. persimi as well as D. fordii. There was distinct differences in D. alata, the genetic similarity coefficient was resulted from 0.672 9 to 0.990 7. With UPGMA clustering method, 16 samples of D. alata could be divided into 4 groups. After comparing samples with the phenotypic characteristics of original plants, it showed that the color and the number of tuber were the most important characteristics of judging the genetic relationship of D. alata. It is concluded that the genetic variation of Dioscorea spp is significant, especially the genetic diversity in D. alata were in a high level. This article supplied a molecular biologic support for distinguishing Dioscorea spp, and also provided basis for breeding of D. alata.
DNA, Plant ; genetics ; Dioscorea ; classification ; genetics ; Genetic Variation ; Phylogeny ; Repetitive Sequences, Nucleic Acid

URP primers of 20 mer derived from repetitive sequence of rice were used to assess genetic variation of oyster mushroom consisting of 10 cultivars of Pleurotus ostreatus, two cultivars of P. florida and two cultivars of P. sajor-caju which were registered in Korea. URP2F and URP38F primers produced cultivar-specific PCR polymorphic bands in the Pleurotus species. UPGMA cluster analysis using the URP-PCR data showed that 14 Pleurotus cultivars are genetically clustered into large three groups. The URP-PCR data provided important information for more efficient breeding strategies of Pleurotus cultivars.
Breeding ; Dermatoglyphics* ; Florida ; Genetic Variation ; Korea* ; Ostreidae* ; Pleurotus* ; Polymerase Chain Reaction ; Repetitive Sequences, Nucleic Acid