• Parasites, Hosts and Diseases
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• v.55 no.6
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• pp.601-606
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• 2017

Cystoisospora is responsible for morbidity in immunocompromised patients. PCR is sensitive for diagnosing Cystoisospora; however, it needs reevaluation for differential molecular diagnosis of cystoisosporiasis. We aimed at evaluating melting curve analysis (MCA) after real-time PCR (qPCR) in diagnosis and genotyping of Cystoisospora as an alternative to conventional PCR. We included 293 diarrheic stool samples of patients attending the Department of Clinical Oncology and Nuclear Medicine of Cairo University Hospitals, Egypt. Samples were subjected to microscopy, nested PCR (nPCR), and qPCR targeting the internal transcribed spacer 2 region (ITS2) of the ribosomal RNA (r RNA) gene followed by melting temperatures ($T_ms$) analysis and comparing the results to PCR-RFLP banding patterns. Using microscopy and ITS2-nPCR, 3.1% and 5.8% of cases were Cystoisospora positive, respectively, while 10.9% were positive using qPCR. Genotyping of Cystoisospora by qPCR-MCA revealed 2 genotypes. These genotypes matched with 2 distinct melting peaks with specified $T_ms$ at $85.8^{\circ}C$ and $88.6^{\circ}C$, which indicated genetic variation among Cystoisospora isolates in Egypt. Genotype II proved to be more prevalent (65.6%). HIV-related Kaposi sarcoma and leukemic patients harbored both genotypes with a tendency to genotype II. Genotype I was more prevalent in lymphomas and mammary gland tumors while colorectal and hepatocellular tumors harbored genotype II suggesting that this genotype might be responsible for the development of cystoisosporiasis in immunocompromised patients. Direct reliable identification and differentiation of Cystoisospora species could be established using $qPCR-T_ms$ analysis which is useful for rapid detection and screening of Cystoisospora genotypes principally in high risk groups.

• Plant Resources
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• v.1 no.2
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• pp.81-91
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• 1998

Fifty-nine Korean soybean (Glycine max L. Merr.) landrace accessions were tested for genotype fingerprinting, differentiation and association between morphological traits and SSR profile. Using 8 SSR loci, 59 varieties were divided into 55 groups, and only 4 pairs of varieties were not uniquely identified. The resolving power of SSR for soybean genotyping was much higher than that of the morphological traits that were studied. Identification efficiency also differed among SSR loci. Those loci with higher numbers of alleles distinguished varieties more effectively. Genetic differentiation values of the soybean landraces varied from 0.57 to 0.82 with a mean of 0.68. The number of alleles detected by the 8 loci ranged from 3 to 8. and the effective number of alleles ranged from 2.3 to 5.1. In a study of the association of SSR alleles with morphological traits, some alleles seemed to be related with some specific morphological traits. Comparison of two kinds of dendrograms which were derived from SSR markers and quantitative traits indicated that the dendrograms were not consistent. Considering the correlation between single SSR locus and qualitative traits governed by major genes, the data suggest that alleles of microsatellite loci be more closely related to some traits determined by major genes than those determined by minor genes.

• Journal of Plant Biotechnology
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• v.33 no.4
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• pp.289-295
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• 2006

This study was carried out to evaluate the suitability of simple sequence repeat (SSR) markers for varietal identification and genetic diversity in 28 commercial tomato varieties. The relationship between marker genotypes and 28 varieties was analyzed. Of the 219 pairs of SSR primers screened against ten tomato varieties, 18 pairs were highly polymorphic with polymorphism information content (PIC) ranging from 0.467 to 0.800. Among the polymorphic loci, two to nine SSR alleles were detected for each locus with an average of 3.3 alleles per locus. Genetic distances were estimated according to Jaccard's methods based on the probability that the amplified fragment from one genotype would be present in another genotype. These varieties were categorized into cherry and classic fruit groups corresponding to varietal types and genetic distance of cluster ranging from 0.35 to 0.97. The phonogram discriminated all varieties by marker genotypes. The SSR markers proved to be useful variety identification and genetic resource analysis of tomato.

• Food Science of Animal Resources
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• v.24 no.4
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• pp.355-360
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• 2004

In Korean beef market, one of the major problems is mislabeling or fraudulent distribution of Holstein dairy meat or imported beef as domestic Hanwoo meat. Therefore, there has been a great need for a development of technology to identify beef breeds in meat and meat products. This study was carried out to develop the accurate and reliable method for the identification of beef breed using PCR-RFLP marker of MC1R, MGF and TYRPl genes affecting coat colors in cattle. A single base substitution (G\longrightarrowT transition) at the codon for amino acid position 104 of MC1R gene was identified between Hanwoo and Holstein and Angus breeds. The change at this position creates Msp I restriction site in Holstein and Angus, but not in Hanwoo. When the DNA amplified products (537 bp) was digested with Msp I, Hanwoo meat showed a single band of 537bp, while two fragments of 329bp and 208 bp were observed in Holstein meat and Angus breed, respectively. Thus, breed-specific RFLP marker in the MC1R gene can be used to distinguish between Hanwoo meat and Holstein and Angus meats. In the RFLP genotype of MGF gene, the frequency of r/r type was 75％ in Manwoo, whereas the frequency of R/R was 80％ in Hereford breed. Holstein and Angus breeds showed 100％ for R/r type. Therefore, Hanwoo meat showed significant difference in the MGF genotype frequencies compared with those of Holstein meat and imported beef cattle breeds. However, TYRP1 gene showed the same genotype in all breeds examined. Thus, this TYRP1 gene can not be used as a molecular marker for breed identification. As a consequence, we suggest that RFLP markers of the MC1R and MGF coat color genes could be used as DNA marker for identification of Hanwoo meat from Holstein and imported meats.

• Journal of Sasang Constitutional Medicine
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• v.10 no.2
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• pp.283-290
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• 1998

Sasang Constitutional Medicine focuses on the different constitutional manifestations of the individual's nature and emotions. The nature and emotions drive the ascending and descending of Qi in the body. And this dynamics of the Qi's ascent and descent shapes the different types of structures, functions and temperaments. Although Sasang Constitutional Medicine has many advantages, its diagnosis of the constitution still depends on the doctors' own idea and has no objective identification. So many doctors in Korea have been trying to solve this problem. Recently, there are several efforts to find out the relationship between genetic information and constitution. By the way, May, 1998 there is a astonishing report about the gene which determines the human performance, that is ACE(angiotensin converting enzyme). And it suggests that the I allele was associated with improved endurance performance. ACE has three genotype including II, ID and DD. "I" means insertion and "D" means deletion. We determined the type of the Sasang constitution with QSCCII questionaire and the one's ACE genotype with PCR of the 127 people and we discovered the relationship between the constitution and the ACE genotype. The result is as follow. Among 39 people who have the II genotype, 7(18%) belong to Taeum(Taiyin), 9(23.1%) belong to Soyang(Shaoyang) and 23(59%) belong to Soeum(Shaoyin). Among 62 people who have the ID genotype, 18(29%) belong to Taeum(Taiyin), 21(33.9%) belong to Soyang(Shaoyang) and 23(37.1%) belong to Soeum(Shaoyin). Among 26 people who have DD genotype, 11(42.3%) belong to Taeum(Taiyin), 4(15.4%) belong to Soyang(Shaoyang) and 11(42.3%) belong to Soeum(Shaoyin). This data indicates that there are implicable relationship between the Sasang constitution and ACE genotype. Especially people who have II genotype have much possibility to be a Soeum(Shaoyin) person (59%) and Soyang(Shaoyang) person have less possibility to have DD genotype (15.4%). With this conclusion, we suggest further study of relationship between the Sasang constitution and ACE genotype and we think that other polymorphism can be a candidate of the partner of Sasang constitution.

• Journal of Oral Medicine and Pain
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• v.21 no.2
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• pp.317-329
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• 1996

Allelic frequency and genotype distribution of short tandem repeat(STR) F13A01 locus was analysed by polymerase chain reaction, polyacrylamide gel electrophoresis and silver staining from human genomic deoxyribonucleic acid(DNA) was extracted from 205 unrelated Korean to be applied to forensic identification and parentage testing as a database. The results were as follows : 1. 5 alleles and 11 genotypes of F13A01 locus were detected and heterozygosity value was 62.0% and the observed each alleles and allelic frequency was 3.2(0.363), 4(0.105), 5(0.063), 6(0.466), 16(0.002). 2. The allelic diversity value was 0.639 and the power of discrimination was 0.804.3. Compared with observed number of alleles and allele frequency in ethnic difference, result was appeared to be similar to that of Japanese and Asians, while was appeared to be much different to that of Blacks and Caucasians in the observed number of alleles and frequency of allele 3.2, 5, 7. From the above result of this investigation, the allelic frequency of STR F13A01 locus in the Korean was considerd to be useful for individual identification and parentage testing as a database.

• Proceedings of the Korean Statistical Society Conference
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• 2005.11a
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• pp.31-36
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• 2005

An identification and characterization of susceptibility genes for common complex multifactorial diseases is a challengeable task, in which the effect of single genetic variation will be likely dependent on other genetic variations(gene-gene interaction) and environmental factors (gene-environment interaction). To address is issue, the multifactor dimensionality reduction (MDR) has been proposed and implemented by Ritchie et al. (2001), Moore et al. (2002), Hahn et al.(2003) and Ritchie et al. (2003). With MDR, multilocus genotypes effectively reduce the dimension of genotype predictors from n to one, which improves the identification of polymorphism combinations associated with disease risk. However, MDR cannot handle missing observations appropriately, in which missing observation is treated as an additional genotype category. This approach may suffer from a sparseness problem since when high-order interactions are considered, an additional missing category would make the contingency table cells more sparse. We propose a new MDR approach with minimum loss of sample sizes by considering missing data over all possible multifactor classes. We evaluate the proposed MDR by using the prediction errors and cross validation consistency.

• Molecules and Cells
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• v.21 no.2
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• pp.302-307
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• 2006

Two Epstein-Barr virus (EBV) types, type 1 and type 2, maintain the same allelic specificity at four genomic loci encoding the EBNA2, -3A, -3B, and -3C proteins. We have previously described 16 EBV-transformed B-lymphoblastoid cell lines derived from Korean cancer patients, and the EBNA2 types of the EBV isolates therein. In this study, the allelic types of the EBNA2, -3A, -3B, and -3C genes of these EBV isolates were determined. We report the identification of two distinct types of naturally occurring intertypic recombinants, one with genotype EBNA2 type1/EBN3A, -3B, -3C type 2 and the other with genotype EBNA2, -3A type 1/EBNA3B, -3C type 2. The existence of these intertypic recombinants indicates that various intertypic EBV strains may be circulating in the human population, in addition to typical EBV-1 and EBV-2 strains.

• Asian-Australasian Journal of Animal Sciences
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• v.24 no.11
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• pp.1504-1513
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• 2011

It is important to identify genetic interactions related to human diseases or animal traits. Many linear statistical models have been reported but they did not consider genetic interactions. Genotype matrix mapping (GMM) has been developed to identify genetic interactions. This study uses the GMM method to detect superior SNP combinations of the CCDC158 gene that influences average daily gain, marbling score, cold carcass weight and longissimus muscle dorsi area traits in Hanwoo. We evaluated the statistical significance of the major SNP combinations selected by implementing the permutation test of the F-measure. The effect of g.34425+102 A>T (AA), g.8778G>A (GG) and g.4102+36T>G (GT) SNP combinations produced higher performance of average daily gain, marbling score, cold carcass weight and the longissimus muscle dorsi area traits than the effect of a single SNP. GMM is a fast and reliable method for multiple SNP analysis with potential application in marker-assisted selection. GMM may prospectively be used for genetic assessment of quantitative traits after further development.

• The Korean Journal of Applied Statistics
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• v.29 no.7
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• pp.1247-1255
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• 2016

Kim and Lee (2015) identified a superior FABP4 gene that improves the grade and fatty acid of Korean cattle. This study selects a superior genotype by expanding genes that influence the economic traits of Korean cattle. Expanded genes are FABP4, SCD, FASN and SREBPs that are related to grade and fatty acid (Oh, 2014). We use the adjusted economic-trait values with environmental factors excluded. We also applied multifactor dimensionality reduction(MDR) method to data of the adjusted economic-trait values. As a result, we identified superior genes and genotypes which improved the grade and fatty acid of Korean cattle.