• Reproductive and Developmental Biology
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• v.38 no.3
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• pp.123-127
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• 2014

This study was conducted for SNPs in the 5'-regions of estrogen receptor-${\alpha}$ (ESR-${\alpha}$), and association with calving interval (CI), service per conception (SPC) and 305 days milk yield in Hanwoo and Holstein dairy cattle. The genetic improvement was incurred low reproduction performance. The objective of this study was to investigate connections between single nucleotide polymorphisms (SNP) of Estrogen receptor-${\alpha}$ (ESR-${\alpha}$) with reproduction performance (calving interval, service per conception, and 305 d milk yield) in Hanwoo and Holstein dairy cattle. Hanwoo and Holstein blood samples were collected from 183 and 124 dam of breeding farms and DNA was extracted. Primer design was based on NCBI GenBank (Accession No. AY340579). The PCR-RFLP method with Bgl I was used to genotype the cattle. The result showed two variants of the ESR-${\alpha}$ gene. The Bgl I cut the 492 bp amplification product into 322 bp and 170 bp fragments for allele G, while allele A remained uncut, resulting in two restriction fragments for homozygote G/G and three fragments for heterozygote A/G. We found two of different genotypes in these breeds, A/G and G/G. In Hanwoo, the A/G genotype frequency was 0.13, and G/G was 0.87. The CI of A/G was $382.18{\pm}10.03$ days, and G/G was $381.69{\pm}5.22$ days. The SPC of A/G was $1.62{\pm}0.16$, and G/G was $1.32{\pm}0.04$. While CI showed no significance difference, SPC exhibited significant difference (p<0.05). In Holstein cattle, the frequency of genotype A/G was 0.02 and G/G was 0.98. The 305 days milk yield of A/G was $7,253.00{\pm}936.00kg$ and of G/G was $8,747.51{\pm}204.88kg$, showing no significant difference.

• Clinical and Experimental Pediatrics
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• v.52 no.2
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• pp.187-193
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• 2009

Purpose : Adiponectin is a molecule that plays an important role in the metabolic syndrome. In addition, its concentration is known to be decreased in obesity, type 2 diabetes, and coronary artery disease. Although a relationship between hypertension and serum adiponectin concentrations has been reported by several authors, such findings continue to be debated. We investigated whether hypoadiponectinemia is related to hypertension in adolescents and studied the associated genetic polymorphism. Methods : Forty hypertensive adolescents (Age 16-17 years old) and twenty normotensive matched subjects were included. Serum adipo-nectin, insulin, renin, aldosterone and angiotensin converting enzyme (ACE) levels were compared. Their carotid intima-media thickness (cIMT) and pulse wave velocity (PWV) were measured. Polymorphisms of the adiponectin I164T gene were investigated using polymerase chain reaction (PCR). Results : The hypertensive adolescents had significantly greater cIMT and PWV. In addition, the serum aldosterone, renin and insulin levels were significantly higher in the hypertensive group. The plasma concentrations of adiponectin did not differ significantly between the two groups. TC genotype was not found in our study subjects; they all had the TT genotype of the adiponectine gene. Conclusion : The results of our study showed that adiponectin levels were not significantly different in adolescents with hypertension. There was no distinctive genetic polymorphism observed in this group of patients. Further large scale studies are needed to clarify the association between genetic variations and adiponectin in hypertensive adolescents.

• Parasites, Hosts and Diseases
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• v.55 no.5
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• pp.473-480
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• 2017

Plasmodium vivax merozoite surface protein-1 (PvMSP1) gene codes for a major malaria vaccine candidate antigen. However, its polymorphic nature represents an obstacle to the design of a protective vaccine. In this study, we analyzed the genetic polymorphism and natural selection of the C-terminal 42 kDa fragment within PvMSP1 gene ($PvMSP1_{42}$) from 77 P. vivax isolates, collected from imported cases of China-Myanmar border (CMB) areas in Yunnan province and the inland cases from Anhui, Yunnan, and Zhejiang province in China during 2009-2012. Totally, 41 haplotypes were identified and 30 of them were new haplotypes. The differences between the rates of non-synonymous and synonymous mutations suggest that $PvMSP1_{42}$ has evolved under natural selection, and a high selective pressure preferentially acted on regions identified of $PvMSP1_{33}$. Our results also demonstrated that $PvMSP1_{42}$ of P. vivax isolates collected on China-Myanmar border areas display higher genetic polymorphisms than those collected from inland of China. Such results have significant implications for understanding the dynamic of the P. vivax population and may be useful information towards China malaria elimination campaign strategies.

• Asian-Australasian Journal of Animal Sciences
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• v.33 no.11
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• pp.1725-1731
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• 2020

Objective: An initial RNA-Sequencing study revealed that UDP-galactose-4-epimerase (GALE) was one of the most promising candidates for milk protein concentration in Chinese Holstein cattle. This enzyme catalyzes the interconversion of UDP-galactose and UDP-glucose, an important step in galactose catabolism. To further validate the genetic effect of GALE on milk protein traits, genetic variations were identified, and genotypes-phenotypes associations were performed. Methods: The entire coding region and the 5'-regulatory region (5'-UTR) of GALE were re-sequenced using pooled DNA of 17 unrelated sires. Association studies for five milk production traits were performed using a mixed linear animal model with a population encompassing 1,027 Chinese Holstein cows. Results: A total of three variants in GALE were identified, including two novel variants (g.2114 A>G and g.2037 G>A) in the 5'-UTR and one previously reported variant (g.3836 G>C) in an intron. All three single nucleotide polymorphisms (SNPs) were associated with milk yield (p<0.0001), fat yield (p = 0.0006 to <0.0001), protein yield (p = 0.0232 to <0.0001) and protein percentage (p<0.0001), while no significant associations were detected between the SNPs and fat percentage. A strong linkage disequilibrium (D' = 0.96 to 1.00) was observed among all three SNPs, and a 5 Kb haplotype block involving three main haplotypes with GAG, AGC, and AGG was formed. The results of haplotype association analyses were consistent with the results of single locus association analysis (p<0.0001). The phenotypic variance ratio above 3.00% was observed for milk protein yield that was explained by SNP-g.3836G >C. Conclusion: Overall, our findings provided new insights into the polymorphic variations in bovine GALE gene and their associations with milk protein concentration. The data indicate their potential uses for marker-assisted breeding or genetic selection schemes.

• Molecules and Cells
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• v.38 no.5
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• pp.466-473
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• 2015

Over the last 30 years, Hanwoo has been selectively bred to improve economically important traits. Hanwoo is currently the representative Korean native beef cattle breed, and it is believed that it shared an ancestor with a Chinese breed, Yanbian cattle, until the last century. However, these two breeds have experienced different selection pressures during recent decades. Here, we whole-genome sequenced 10 animals each of Hanwoo and Yanbian cattle (20 total) using the Illumina HiSeq 2000 sequencer. A total of approximately 3.12 and 3.07 billion sequence reads were mapped to the bovine reference sequence assembly (UMD 3.1) at an average of approximately 10.71- and 10.53-fold coverage for Hanwoo and Yanbian cattle, respectively. A total of 17,936,399 single nucleotide polymorphisms (SNPs) were yielded, of which 22.3% were found to be novel. By annotating the SNPs, we further retrieved numerous nonsynonymous SNPs that may be associated with traits of interest in cattle. Furthermore, we performed whole-genome screening to detect signatures of selection throughout the genome. We located several promising selective sweeps that are potentially responsible for economically important traits in cattle; the PPP1R12A gene is an example of a gene that potentially affects intramuscular fat content. These discoveries provide valuable genomic information regarding potential genomic markers that could predict traits of interest for breeding programs of these cattle breeds.

• Journal of Animal Science and Technology
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• v.46 no.6
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• pp.937-946
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• 2004

Duroc is widely used to improve the meat quality and productivity. To elucidate the phylogenetic relation and the sequence specificity for the maternal property, the complete sequence of mitochondrial genome was determined and the population diversity of Duroc was investigated in this study. The length of mtDNA tested is 16,584-bp. There are several insertion/deletion mutations in the control region and coding regions for tRNA and rRNA, respectively, but not in peptide-coding regions. Four peptide-coding genes(COⅡ, COⅢ, ND3 and ND4) showed incomplete termination codon sequences such as T--, and two(ND2 and ND4L) did alternative initiation codons(AIC), respectively. Especially, the initiation codon sequences of ND2 gene were polymorphic in this population. Polymorphisms were detected in 11-bp duplication motif within control region as well as ND2 and CYTB. Variation patterns observed from the tests on three mtDNA regions were linked completely and then two haplotypes obtained from combining the data dividing this population. Duroc mtDNA is observed at the European pig cluster in the phylogenetic tree, however, the results from the population analyses supported previous opinions. This study suggests that the breed Duroc was mainly originated from the European pig lineage, and Asian lineage was also used to form the pig breed Duroc as maternal progenitors.

• 한국균학회소식:학술대회논문집
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• 2015.11a
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• pp.41-41
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• 2015

Oomycetes belong to the kingdom Straminipila, a remarkably diverse group which includes brown algae and planktonic diatoms, although they have previously been classified under the kingdom Fungi. These organisms have evolved both saprophytic and pathogenic lifestyles, and more than 60% of the known species are pathogens on plants, the majority of which are classified into the order Peronosporales (includes downy mildews, Phytophthora, and Pythium). Recent phylogenetic investigations based on DNA sequences have revealed that the diversity of oomycetes has been largely underestimated. Although morphology is the most valuable criterion for their identification and diversity, morphological species identification is time-consuming and in some groups very difficult, especially for non-taxonomists. DNA barcoding is a fast and reliable tool for identification of species, enabling us to unravel the diversity and distribution of oomycetes. Accurate species determination of plant pathogens is a prerequisite for their control and quarantine, and further for assessing their potential threat to crops. The mitochondrial cox2 gene has been widely used for identification, taxonomy and phylogeny of various oomycete groups. However, recently the cox1 gene was proposed as a DNA barcode marker instead, together with ITS rDNA. To determine which out of cox1 or cox2 is best suited as universal oomycete barcode, we compared these two genes in terms of (1) PCR efficiency for 31 representative genera, as well as for historic herbarium specimens, and (2) in terms of sequence polymorphism, intra- and interspecific divergence. The primer sets for cox2 successfully amplified all oomycete genera tested, while cox1 failed to amplify three genera. In addition, cox2 exhibited higher PCR efficiency for historic herbarium specimens, providing easier access to barcoding type material. In addition, cox2 yielded higher species identification success, with higher interspecific and lower intraspecific divergences than cox1. Therefore, cox2 is suggested as a partner DNA barcode along with ITS rDNA instead of cox1. Including the two barcoding markers, ITS rDNA and cox2 mtDNA, the multi-locus phylogenetic analyses were performed to resolve two complex clades, Bremia lactucae (lettuce downy mildew) and Peronospora effuse (spinach downy mildew) at the species level and to infer evolutionary relationships within them. The approaches discriminated all currently accepted species and revealed several previously unrecognized lineages, which are specific to a host genus or species. The sequence polymorphisms were useful to develop a real-time quantitative PCR (qPCR) assay for detection of airborne inoculum of B. lactucae and P. effusa. Specificity tests revealed that the qPCR assay is specific for detection of each species. This assay is sensitive, enabling detection of very low levels of inoculum that may be present in the field. Early detection of the pathogen, coupled with knowledge of other factors that favor downy mildew outbreaks, may enable disease forecasting for judicious timing of fungicide applications.

• Journal of the Korean Chemical Society
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• v.51 no.6
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• pp.543-548
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• 2007

Maturity-onset diabetes of the young (MODY) is a genetically heterogeneous subtype of Type 2 diabetes characterized (non-insulin-dependent) by early onset, usually before 25 years of age, autosomal dominant inheritance and a primary defect in insulin secretion. Mutations in the glucokinase (GCK) and hepatocyte nuclear factor (HNF)-1α genes are the major causes of monogenic forms of Type 2 diabetes mellitus. Therefore it is need to study relation with these polymorphisms by diverse analysis methods. The promotor and coding regions inclusive intron exon boundaries of the GCK, HNF-1α genes were examined by PCR-DHPLC (Polymerase Chain Reaction - Denaturing High Performance Liquid Chromatography) and direct sequencing. We extracted DNA from 11 patients and 20 normals. Then we confirmed a single-nucleotide polymorphism using PCR-DHPLC. As results, we identified one mutation (R135G) in GCK gene and two mutations (I27L, S487N) in HNF-1a and at the same time detected mutation in intron 8.

• Journal of Life Science
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• v.25 no.3
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• pp.257-262
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• 2015

The genetic variability of four species of the genus Zoysia collected from South Korea was analyzed using an inter-simple sequence repeat (ISSR) marker system. Polymerase chain reactions (PCR) with eight ISSR primers generated 86 amplicons, 76 (87.1%) of which were polymorphisms. The polymorphism information content (PIC) value of the ISSR marker system was 0.848. The percentage of polymorphic loci (P_p) ranged from 41.2% to 44.7%. Nei’s gene diversity (H) ranged from 0.149 to 0.186, with an average overall value of 0.170. The mean of Shannon’s information index (I) value was 0.250. Total genetic diversity values (H_T) varied between 0.356 (ISSR-1) and 0.418 (ISSR-16), for an average overall polymorphic loci of 0.345. Interlocus variation in within-species genetic diversity (H_S) was low (0.170). On a per-locus basis, the proportion of total genetic variation due to differences among species (G_ST) was 0.601. This indicated that about 60.1% of the total variation was among species. Thus, about 39.9 of genetic variation was within species. The estimate of gene flow, based on G_ST, was very low among species of the genus Zoysia (N_m = 0.332). The phylogenic tree showed three distinct groups: Z. macrostachya and Z. tenuifolia clades and other species were formed the separated clusters. In conclusion, the ISSR assay was useful for detecting genetic variation in the genus Zoysia, and its discriminatory power was comparable to that of other genotyping tools.

• Journal of Periodontal and Implant Science
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• v.34 no.3
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• pp.623-637
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• 2004

중증 만성 치주염과 1L-1B+3954 및 1L-1A+4845 유전자의 대립유전자 2 보유 유전자 다변성이 관련된다고 보고되었다. 그러나 이러한 1L-1 복합유전자 다변성과 만성 치주염 및 급진성 치주염과의 관련성에 대해서는 상반되게 보고되고 있는데 이는 인종적 배경과 질환특성의 차이에 기인한 것으로 보인다. 이 연구는 한국인에서 경도, 중등도와 중증의 만성 치주염 그리고 급진성 치주염 환자를 대상으로 하여 1L-1A+4845, 1L-1B+3954, 1L1B-511, 1L-1 RN intron 2 (VNTR) 유전자 다변성의 분포를 평가하고, 치주질환의 심도와 유형에 관련되는지 알아보고자 시행되었다. 전남대학교 병원 치주과에서 검진과 치료를 받은 100명의 치주질환자를 대상으로 하였고 질환군은 치주낭 깊이, 부착 소실, 골 소실을 기준으로 하여 경도, 중등도, 중증의 만성 치주염, 급진성 치주염군으로 분류하였다. 대조군으로는 전남대학교 병원 소아치과에 내원한 전신적으로 건강한 92명의 아동을 포함하였다. 각 대상 환자에서 채취된 협점막상피에서 genomic DNA를 얻어 1L-1A+4845, 1L-1B+3954, 1L-1B-511 genotype은 중합효소 연쇄반응을 시행한 후 제한 효소분해과정을 거쳐 전기영동 후 분리한 결과를 해석하였으며 1L-1 RN(VNTR) 유전형은 중합효소연쇄반응 후 분리한 결과를 해석하여 다음의 결과를 얻었다. 대립유전자 2 보유자 비율은 치주질환자에서 1L-1A+4845, 1L-1B+3954, 1L-1B-511, 1L-1 RN이 각각 61%, 13%, 76.6%, 34%였으며 대조군에서는 76.9%, 7.7%, 62.2%, 19.1%였다. 1L-1B+3954과 1L-1A+4845 대립유전자 2 보유자인 양성유전자형 비율은 경도, 중등도, 중증의 만성치주염, 급진성 치주염환자에서 각각 10%, 7.9%, 22.2%, 12% 였으며 치주질환자의 13%, 대조군의 7.7%에서 양성 복합유전자형(positive genotype)을 보였다. IL-1B-511 유전자 다변성은 치주질환자에서 대조군에 비하여 높았으며 급진성 치주염환자에서 대립유전자 2 보유자율이 유의하게 높았다(p<0.01). IL-1 RN intron 2 유전자 다변성은 중등도 및 중증 만성 치주염환자에서 대립유전자 2 보유자율이 유의하게 증가하였다. 이러한 결과는 IL-1 gene cluster의 유전형이 한국인에서도 치주염의 유형과 질환 심도에 관련될 수 있음을 시사하였다.