• Asian-Australasian Journal of Animal Sciences
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• v.29 no.5
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• pp.607-614
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• 2016

The objectives of the study were to estimate genetic parameters for milk production traits of Holstein cattle using random regression models (RRMs), and to compare the goodness of fit of various RRMs with homogeneous and heterogeneous residual variances. A total of 126,980 test-day milk production records of the first parity Holstein cows between 2007 and 2014 from the Dairy Cattle Improvement Center of National Agricultural Cooperative Federation in South Korea were used. These records included milk yield (MILK), fat yield (FAT), protein yield (PROT), and solids-not-fat yield (SNF). The statistical models included random effects of genetic and permanent environments using Legendre polynomials (LP) of the third to fifth order (L3-L5), fixed effects of herd-test day, year-season at calving, and a fixed regression for the test-day record (third to fifth order). The residual variances in the models were either homogeneous (HOM) or heterogeneous (15 classes, HET15; 60 classes, HET60). A total of nine models (3 orders of $polynomials{\times}3$ types of residual variance) including L3-HOM, L3-HET15, L3-HET60, L4-HOM, L4-HET15, L4-HET60, L5-HOM, L5-HET15, and L5-HET60 were compared using Akaike information criteria (AIC) and/or Schwarz Bayesian information criteria (BIC) statistics to identify the model(s) of best fit for their respective traits. The lowest BIC value was observed for the models L5-HET15 (MILK; PROT; SNF) and L4-HET15 (FAT), which fit the best. In general, the BIC values of HET15 models for a particular polynomial order was lower than that of the HET60 model in most cases. This implies that the orders of LP and types of residual variances affect the goodness of models. Also, the heterogeneity of residual variances should be considered for the test-day analysis. The heritability estimates of from the best fitted models ranged from 0.08 to 0.15 for MILK, 0.06 to 0.14 for FAT, 0.08 to 0.12 for PROT, and 0.07 to 0.13 for SNF according to days in milk of first lactation. Genetic variances for studied traits tended to decrease during the earlier stages of lactation, which were followed by increases in the middle and decreases further at the end of lactation. With regards to the fitness of the models and the differential genetic parameters across the lactation stages, we could estimate genetic parameters more accurately from RRMs than from lactation models. Therefore, we suggest using RRMs in place of lactation models to make national dairy cattle genetic evaluations for milk production traits in Korea.

• Korean Journal of Medicinal Crop Science
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• v.11 no.5
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• pp.377-384
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• 2003

Genetic differences among nine land races of Korean ginseng (Panax ginseng C. A. Meyer) were examined using RAPD markers. Land races of Korean ginseng were collected from nine regions in Korea: Cheongwon, Guesan, Geumsan, Namwon, Pochun, Yangju, Yeoncheon, Yeongju. Out of 48 RAPD primers tested, 5 primers (OPA 7, OPA 13, URP 2, URP 3 and UBC 3) produced remarkable bands which showing polymorphisms among evaluated collections. Lower levels of genetic diversity were in detected same land races than among other land races. Genetic differences within and among land races indicate heterogeneity. These results indicate that cultivated ginseng in Korea is heterogeneous. Genetic similarity matrices of RAPD profiles were generated via coefficients of variation and the data were processed by the cluster analysis (UPGMA). When 90 collections were evaluated using selected 5 primers, those were clustered to 5 and 3 subgroups. These differences in genetic variation between land races of Korean ginseng implied the potential source for further breeding of Korean ginseng.

• Genomics & Informatics
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• v.6 no.1
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• pp.29-31
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• 2008

Single nucleotide polymorphisms (SNPs) in the promoter region of the IL-1B (interleukin-1) gene have been implicated in a variety of diseases that have an inflammatory component. However, there has been significant heterogeneity among study results, especially between Caucasian and Asian populations. Recently, it has been reported that SNPs in the IL-1B gene affect transcription, according to haplotype context, and genetic association studies may be more informative if functional SNP haplotypes of population are analyzed. Therefore, we estimated the distribution of IL-1B promoter haplotypes in 433 Koreans using the three major functional IL-1B promoter SNPs (IL-1B -1464, -511, and -31) and compared the results with those in Caucasians. The difference in IL-1B promoter haplotype frequency between Korean and Caucasian populations was statistically significant. The potentially more inflammatory haplotypes had higher frequencies in Koreans when compared with Caucasians. These Korean haplotype data will be useful for future association studies between IL-1B SNPs and disease risk.

• Animal cells and systems
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• v.10 no.2
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• pp.65-71
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• 2006

Autosomal Dominant Polycystic Kidney Disease (ADPKD) is one of the most common inherited renal disorders in the world. Mutations in PKD1 located on chromosome 16p13.3 are responsible for 85% of all the ADPKD patients whereas mutations in PKD2 on chromosome 4q21-23 are responsible for the rest of the cases. Genetic heterogeneity and the problems of mutation detection in PKD1 suggest that linkage analysis is an important approach to study the genetics of ADPKD. To evaluate the availability of six (CA)n microsatellite markers for the linkage analysis of ADPKD in the Korean population, we examined the allele frequencies and heterozygosities of the markers. With the exception of KG8, five markers were highly informative, with PIC values over 0.5, but the PIC value of KG8 marker was less informative than other five markers because of the low number of alleles. Therefore, this study will be useful in linkage analysis for ADPKD families in the Korean population.

• Proceedings of the Korean Society of Crop Science Conference
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• 2017.06a
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• pp.31-31
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• 2017

Understanding the mechanism(s) to overcome or prevent seed ageing deterioration during storage is of fundamental interest to seed physiologists. Vitamin E (tocols) is known as a key metabolite to efficiently scavenge lipid peroxy radicals which cause membrane breakdown resulting in seed ageing. However, in rice research this hypothesis has been tested for very few lines only without considering intraspecific variation in genomic structure. Here, we present a correlation study between tocols and seed longevity using a diverse rice panel. Seeds of 20 rice accessions held in the International Rice Genebank at the International Rice Research Institute, representing aus, indica, temperate japonica and tropical japonica subpopulations, were used for tocols analysis (quantification of ${\alpha}$-, ${\beta}$-, ${\gamma}$-, ${\delta}$-tocopherol/tocotrienol by ultra performance liquid chromatography) and storage experiments at $45^{\circ}C$ and 10.9% seed moisture content (sample taken for germination testing every 3 days up to 60 days). To examine interactions between DNA sequences and phenotype, the 700k high-density single-nucleotide polymorphism marker data-set was utilized. Both seed longevity (time for viability to fall to 50%; $p_{50}$) and tocols content varied across subpopulations due to heterogeneity in the genetic architecture. Among eight types of tocol homologues, ${\alpha}$-tocopherol and ${\gamma}$-tocotrienol were significantly correlated with $p_{50}$ (negatively and positively, respectively). While temperate japonica varieties were most abundant in ${\alpha}$-tocopherol, indica varieties recorded 1.3 to 1.7-fold higher ${\gamma}$-tocotrienol than those of other subpopulations. It was highlighted that specific ratio of tocol homologues rather than total tocols content plays an important role in the seed longevity mechanism.

• Korean Journal of Veterinary Service
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• v.32 no.1
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• pp.1-10
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• 2009

In order to obtain the genetic information of the Korean isolates of porcine circovirus 2 (PCV2), complete genomes of five isolates from Korean PCVD weaned pigs with wasting syndromes were sequenced and compared with those of other published PCV2 isolates. Of the five PCV2 isolates, four (1767 nucleotides) were classified into PCV2b, and one (1,768 nucleotides) was PCV2a. Moreover, it appeared that PCV2b is now the dominant genotype circulating in Korea herds. Total complete genomes of four PCV2b isolates shared $99.1{\sim}99.4%$ nucleotide sequence homology each other, and were only $95.4{\sim}96.2%$ similar to one PCV2a isolate. ORF2 genome of four PCV2b isolates shared over 99% nucleotide sequence and deduced amino acid sequence identity to each other. Nevertheless, those were much divergent with the PCV2a isolate of this study and ranged from $92.3{\sim}92.7%$ nucleotide homology and $91.9{\sim}92.3%$ deduced amino acid sequence homology, respectively. The amino acid sequence alignments of the putative capsid protein identified three major regions of amino acid heterogeneity at residues $59{\sim}91$, $121{\sim}136$ and $190{\sim}210$. Two of those correspond with dominant immunoreactive areas. Phylogenetic analysis based on the complete genome of PCV2 isolates showed that four PCV2b isolates of this study existed the closest relationship with European strains (Netherland, UK and France). One PCV2a isolate was closely related to Japan and North America strains.

• Korean Journal of Head & Neck Oncology
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• v.16 no.1
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• pp.3-8
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• 2000

Background and Objectives: Adenoid cystic carcinoma of salivary glands is characterized by insidious growth over many years, local recurrences, and distant metastasis and classified to three distinct histologic subtypes: tubular, cribriform, and solid. The solid type is known to have the worst prognosis. However, histopathologic heterogeneity is observed in tumors from the same patient. We have attempted to elucidate the genotypic differences, characterized by polysomies of chromosome 17, in adenoid cystic carcinoma according to the phenotypic histopathologic heterogeneity. Materials and Methods: Fluorescence in situ hybridization was performed on formalin-fixed paraffin blocks from seven patients with head and neck adenoid cystic carcinoma, using the centromeric $\alpha$-satellite probe of chromosome 17 to detect nuclei exhibiting polysomy. The difference in polysomeric chromosome expression in cribriform, tubular, solid type and type I, II, III according to the Szanto classification was analyzed. Results: Polysomy of chromosome 17 was found in 15.28% of the cribriform type, in 15.68% of the tubular type, and in 18.87% of the solid type. The proportion of polysomy was statistically higher in the solid type than in the cribriform type(p<0.05), and the proportion of polysomy increased progressively from type 1 to type 3, but this trend was statistically insignificant(p>0.05). Conclusion: We suggest that there may be genetic variations in tumor from the same patient depending on the histopathologic heterogenetiy in adenoid cystic carcinomas.

• Journal of Periodontal and Implant Science
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• v.29 no.4
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• pp.963-979
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• 1999

This study examined ribotypes of 36 P. gingivalis strains isolated from 10 rapidly progressive periodontitis patients in Korean and revealed the presence of genetic heterogeneity among the patients. Ribotyping was performed by using a oligonucleotide probes based on 16S rRNA after whole genomic DNA had been digested with the restriction endonuclease enzyme Kpn I and Pst I. In addition, the antigenic heterogeneity of fimbrillin and protease activity was analysed to observe the virulency of P. gingivalis. The results were as follows. 1. Using KpnI, 6 ribotypes were detected, whereas 7 ribotypes were identified by using PstI. When combined two enzymes, a total of 8 ribotypes was subgrouped. 2. Ribotype I/e was the most common and detected in 4 among 10 patients. 3. The fimbrillin expressed from P. gingivalis isolates had the molecular size of 41kDa, 43kDa, 49kDa. It was observed that the size of fimbrillin with the same ribotypes could be identical. 4. All the P. gingivalis strains showed strong proteolytic activity and had the molecular size more than 120kDa. In summary, total 8 ribotypes were observed for isolates from rapidly progressive periodontitis patients. Forty percent of the patients harbored isolates exhibiting the same ribotype I/e, and it was observed that more than one ribotype can coexist in an individual patient.

• Clinical and Experimental Pediatrics
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• v.63 no.2
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• pp.34-43
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• 2020

Phenylketonuria is a disease caused by congenital defects in phenylalanine metabolism that leads to irreversible nerve cell damage. However, its detection in the early days of life can reduce its severity. Thus, many countries have started disease screening programs for neonates. The present study aimed to determine the worldwide prevalence of classic phenylketonuria using the data of neonatal screening studies.The PubMed, Web of Sciences, Sciences Direct, ProQuest, and Scopus databases were searched for related articles. Article quality was evaluated using the Joanna Briggs Institute Critical Appraisal Evaluation Checklist. A random effect was used to calculate the pooled prevalence, and a phenylketonuria prevalence per 100,000 neonates was reported. A total of 53 studies with 119,152,905 participants conducted in 1964-2017 were included in this systematic review. The highest prevalence (38.13) was reported in Turkey, while the lowest (0.3) in Thailand. A total of 46 studies were entered into the meta-analysis for pooled prevalence estimation. The overall worldwide prevalence of the disease is 6.002 per 100,000 neonates (95% confidence interval, 5.07-6.93). The meta-regression test showed high heterogeneity in the worldwide disease prevalence (I²=99%). Heterogeneity in the worldwide prevalence of phenylketonuria is high, possibly due to differences in factors affecting the disease, such as consanguineous marriages and genetic reserves in different countries, study performance, diagnostic tests, cutoff points, and sample size.

• Molecules and Cells
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• v.46 no.10
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• pp.611-626
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• 2023

Acute myeloid leukemia (AML) is a heterogeneous disease caused by distinctive mutations in individual patients; therefore, each patient may display different cell-type compositions. Although most patients with AML achieve complete remission (CR) through intensive chemotherapy, the likelihood of relapse remains high. Several studies have attempted to characterize the genetic and cellular heterogeneity of AML; however, our understanding of the cellular heterogeneity of AML remains limited. In this study, we performed single-cell RNA sequencing (scRNAseq) of bone marrow-derived mononuclear cells obtained from same patients at different AML stages (diagnosis, CR, and relapse). We found that hematopoietic stem cells (HSCs) at diagnosis were abnormal compared to normal HSCs. By improving the detection of the DNMT3A R882 mutation with targeted scRNAseq, we identified that DNMT3A-mutant cells that mainly remained were granulocyte-monocyte progenitors (GMPs) or lymphoid-primed multipotential progenitors (LMPPs) from CR to relapse and that DNMT3A-mutant cells have gene signatures related to AML and leukemic cells. Copy number variation analysis at the single-cell level indicated that the cell type that possesses DNMT3A mutations is an important factor in AML relapse and that GMP and LMPP cells can affect relapse in patients with AML. This study advances our understanding of the role of DNMT3A in AML relapse and our approach can be applied to predict treatment outcomes.