• Korean Journal of Food Science and Technology
• /
• v.50 no.5
• /
• pp.480-485
• /
• 2018

In this study, to identify single nucleotide polymorphisms (SNPs) associated with meat quality in Berkshire pigs, we performed RNA sequencing. A non-synonymous SNP (nsSNP) in the Complement component 9 (C9) gene was identified, and the association between meat quality traits and the C9 genotype was analyzed. The nsSNP in the C9 gene was located at c.942 G>T. In the dominant model, significant associations were observed between the SNP and meat quality traits such as CIE L, collagen content, moisture level, and $pH_{24h}$, whereas in the co-dominant model, significant associations were observed between the SNP and CIE L, collagen content, and protein content. In the recessive model, a significant association between the C9 genotype and the collagen content was observed. In addition, we identified the significant relationship between the C9 genotype and meat quality according to sex. These results indicate that the C9 SNP can be used as a genetic marker for improving pork quality.

• Journal of Genetic Medicine
• /
• v.6 no.1
• /
• pp.74-80
• /
• 2009

Purpose: To assess the value of first-trimester pregnancy-associated plasma protein-A (PAPP-A), nuchal translucency (NT) and second-trimester alpha-fetoprotein (AFP), human chorionic gonadotropin (hCG), unconjugated estriol (uE3), and inhibin-A in predicting pregnancy complications other than fetal aneuploidy. Materials and Methods: A retrospective study in 3,121 singleton pregnancies with integrated testing was performed at Kangnam CHA hospital between January 2005 and December 2006. Baseline characteristics, pregnancy outcomes, and serum marker levels were obtained by review of the medical records. We analyzed the data to identify associations between the integrated screening markers and adverse pregnancy outcomes. Statistical analyses were performed with the SPSS program. Results: In preterm labor and preeclampsia, high AFP, hCG, and inhibin-A levels and low PAPP-A and NT levels were found to be significantly correlated (P<0.05). Elevated second-trimester inhibin-A levels were associated with preeclampsia (odds ratio 2.843), low birth weight (odds ratio 1.446), and preterm labor (odds ratio 1.287), and while decreased first-trimester PAPP-A levels were associated with preeclampsia (odds ratio 0.51) and preterm labor (odds ratio 0.75). Conclusion: First- and second-trimester maternal serum markers screening can be used for predicting high-risk pregnancies.

• Proceedings of the Korean Society of Crop Science Conference
• /
• 2017.06a
• /
• pp.107-107
• /
• 2017

Sweet corns are enjoyed worldwide as processed products and fresh ears. Types of sweet corn are based on the gene(s) involved. The oldest sweet corn type has a gene called "sugary (su)". Sugary-based sweet corn was typically named "sweet corn". With its relatively short shelf life and the discovery of a complementary gene, "sugary enhanced (se)", the sweet corn (su only) was rapidly replaced with another type of sweet corns, sugary enhanced sweet corn, which has recessive homozygous su/su, se/se genotype. With the incorporation of se/se genotype into existing su/su genotype, sugary enhanced sweet corn has better shelf life and increased sweetness while maintaining its creamy texture due to high level of water soluble polysaccharide, phytoglycogen. Super sweet corn as the name implies has higher level of sweetness and better shelf life than sugary enhanced sweet corn due to "shrunken2 (sh2)" gene although there's no creamy texture of su-based sweet corns. Distinction between sh2/sh2 and su/su genotypes in seeds is phenotypically possible. The Involvement of se/se genotype under su/su genotype, however, is visually impossible. The genotype sh2/sh2 is also phenotypically epistatic to su/su genotype when both genotypes are present in an individual, meaning the seed shape for double recessive sh2/sh2 su/su genotype is much the same as sh2/sh2 +/+ genotype. Hence, identifying the double and triple recessive homozygous genotypes from su, se and sh2 genes involves a testcross to single recessive genotype, chemical analysis or DNA-based marker development. For these reasons, sweetcorn breeders were hastened to put them together into one cultivar. This, however, appears to be no longer the case. Sweet corn companies began to sell their sweet corn hybrids with different combinations of abovementioned three genes under a few different trademarks or genetic codes, i.g. Sweet $Breed^{TM}$, Sweet $Gene^{TM}$, Synergistic corn, Augmented Supersweet corn. A total of 49 commercial sweet corn F1 hybrids with B73 as a check were genotyped using DNA-based markers. The genotype of field corn inbred B73 was +/+ +/+ +/+ for su, se and sh2 as expected. All twelve sugary enhanced sweet corn hybrids had the genotype of su/su se/se +/+. Of sixteen synergistic hybrids, thirteen cultivars had su/su se/se sh2/+ genotype while the genotype of two hybrids and the remaining one hybrid was su/su se/+ sh2/+, and su/su +/+ sh2/+, respectively. The synergistic hybrids all were recessive homozygous for su gene and heterozygous for sh2 gene. Among the fifteen augmented supersweet hybrids, only one hybrid was triple recessive homozygous (su/su se/se sh2/sh2). All the other hybrids had su/su se/+ sh2/sh2 for one hybrid, su/su +/+ sh2/sh2 for three hybrids, su/+ se/se sh2/sh2 for three hybrids, su/+ se/+ sh2/sh2 for four hybrids, and su/+ +/+ sh2/sh2 for three hybrids, respectively. What was believed to be a classic super sweet corn hybrids also had various genotypic combination. There were only two hybrids that turned out to be single recessive sh2 homozygous (+/+ +/+ sh2/sh2) while all the other five hybrids could be classified as one of augmented supersweet genotypes. Implication of the results for extension service and sweet corn breeding will be discussed.

• Tuberculosis and Respiratory Diseases
• /
• v.65 no.6
• /
• pp.495-503
• /
• 2008

Background: Epigenetic alterations in certain genes are now known as at least important as genetic mutation in pathogenesis of cancer. Especially abnormal hypermethylation in or near promoter region of tumor suppressor genes (TSGs) are known to result in gene silencing and loss of gene function eventually. The authors tried to search for new lung cancer-specific TSGs which have CpG islands and HpaII sites, and are thought to be involved in carcinogenesis by epigenetic mechanism. Methods: Tumor tissue and corresponding adjacent normal tissue were obtained from 10 patients who diagnosed with non small cell lung cancer (NSCLC) and underwent surgery in Konyang university hospital in 2005. Methylation profiles of promoter region of 21 genes in tumor tissue & non-tumor tissue were examined with HpaII-MspI methylation microarray (Methyl-Scan DNA chip$^{(R)}$, Genomic tree, Inc, South Korea). The rates of hypermethylation were compared in tumor and non-tumor group, and as a normal control, we obtained lung tissue from two young patients with pneumothorax during bullectomies, methylation profiles were examined in the same way. Results: Among the 21 genes, 10 genes were commonly methylated in tumor, non-tumor, and control group. The 6 genes of APC, AR, RAR-b, HTR1B, EPHA3, and CFTR, among the rest of 11 genes were not methylated in control, and more frequently hypermethylated in tumor tissue than non-tumor tissue. Conclusion: In the present study, HTR1B, EPHA3, and CFTR are suggested as possible novel TSGs of NSCLC by epigenetic mechanism.

• Journal of Chest Surgery
• /
• v.37 no.8
• /
• pp.691-701
• /
• 2004

Background: Tissue hypoxia is a characteristic of many human malignant neoplasms, and hypoxia inducible factor-1 (HIF-1) plays a pivotal role in essential adaptive response to hypoxia, and activates a signal pathway for the expression of the hypoxia-regulated genes, resulting in increased oxygen delivery or facilitating metabolic adaptation to hypoxia. Increased level of HIF-1 a has been reported in many human malignancies, but in esophageal squamous cell carcinoma, the influence of HIF-1 a on tumor biology, including neovascularization, is not still defined. Material and Method: The influence of HIF-1 a expression on angiogenic factors, correlation between the tumor proliferation and HIF-1 a expression, interaction of HIF-1 a expression and p53, and correlation between HIF-1 a expression and clinicopathological prognostic parameters were investigated, using immunohistochemical stains for HIF-1 a, VEGF, CD34, p53, and Ki-67 on 77 cases of resected esophageal squamous cell carcinoma. Result: HIF-1 a expression in cancer cells was found in 33 of 77 esophageal squamous cell carcinoma cases. The 33 cases (42.9%) showed positive stain for HIF-1 a. High HIF-1 a expression was significantly associated with several pathological parameters, such as histologic grade (p=0.032), pathological TMN stage (p=0.002), the depth of tumor invasion (p=0.022), regional lymph node metastasis (p=0.002), distant metastasis (p=0.049), and lymphatic invasion (p=0.004). High HIF-1 a expression had significant VEGF immunoreactivity (p=0.008) and Ki-67 labeling index (p<0.001), but was not correlated with microvascular density within tumors (p=0.088). The high HIF-1 a expression was correlated with aberrant p53 accumulation with a marginal significance (p=0.056). The overall 5-year survival rate was 34.9%. The survival rate of patients with a high HIF-1 a expression was worse than that of patients with low-expression tumors (log-rank test, p=0.0001). High HIF-1 a expression was independent unfavorable factors although statistical significance is marginal in multivariate analysis. Conclusion: It is suggested that (1) high HIF-1 a expression in esophageal squamous cell carcinoma is associated with tumor hypoxia, or with genetic alteration in early carcinogenesis and progressive stages, (2) high HIF-1 a expression may be associated with intratumoral neovascularization through HIF-VEGF pathway, and (3) high HIF-1 a expression is associated with poor prognosis in patients with esophageal squamous cell carcinoma and may playa role as biomarker for regional lymph node metastasis.

• Sleep Medicine and Psychophysiology
• /
• v.8 no.2
• /
• pp.107-112
• /
• 2001

Introduction: Narcolepsy, a sleep disorder characterized by excessive daytime sleepiness and cataplexy, is known to be closely associated with the human leukocyte antigen (HLA) DQB1*0602. Several studies have suggested that HLA-DQB1*0602 is strongly linked with narcolepsy-cataplexy. However, no studies have yet been made on whether HLA DQB1*0602 is associated with Korean patients with narcolepsy. This study was designed to investigate the frequency of HLA-DQB1*0602 of Korean patients with narcolepsy. Methods: Twenty patients were selected (mean age: $28.2{\pm}3.0$, 11 men and 9 women). The patients were confirmed to have narcolepsy by the overnight polysomnography and multiple sleep latency test (MSLT) in addition to their clinical history and symptoms at St. Vincent's Hospital and Korea University Hospital Sleep Disorders Clinic. Any subjects co-morbid with other hypersomnic sleep disorders such as sleep apnea or periodic limb movements during sleep were excluded. Clinical data was collected through a semi-structured interview for narcoleptic patients. All patients and 21 control did HLA typing for the presence of DQB1*0602. Results Obtained were as Follows: 1) Mean sleep latency was 2.4 (${\pm}2.0$ minutes) and mean frequency of sleep-onset REM period was 3.0 (${\pm}1.6$) by MSLT. 2) Characteristic symptoms of narcolepsy investigated were as follows: excessive daytime sleepiness (100%), cataplexy (100%), sleep paralysis (60%), hypnagogic hallucination (70%) and disrupted nocturnal sleep (75%). 3) Strong emotional expression such as laughing (80%) and joking (70%) triggered cataplexy which affects the knee and leg region (80%) and jaw region (30%). 4) HLA-DR2 was found in 90% of patients and 35% in controls. The frequency of HLA-DQB1*0602 in patients and controls was 90%, and 24%, respectively. Conclusions: These results, which exhibit high HLA-DQB1*0602 expression in Korean patients with narcolepsy, suggest that HLADQB1*0602 could be a strong genetic marker in narcolepsy.

• Journal of the Korean Chemical Society
• /
• v.53 no.6
• /
• pp.742-748
• /
• 2009

In the meat industry, correct breed information in food labeling is required to assure meat quality. Genetic markers provide corroborating evidence to identify breed. We described the development of DNA markers to discriminate between Korean beef cattle (Hanwoo), Holstein, and mixed cow beefs. As most breeds are standardized for coat colour, the melanocortin 1 receptor (MC1R) gene, involved in the regulation of eu/pheomelanins synthesis, has been suggested as marker for breed traceability of products of animal origin. We also designed sex-determining region Y (SRY) gene specific primers for Y chromosome detection. In this study, fragments of MC1R gene and SRY gene were amplified by multiplex-PCR and subjected to digestion by MspA1I restriction endonuclease. Reaction products were analysised by denaturing high performance liquid chromatography (DHPLC). As a result, we identified 6 DHPLC peak types from MC1R gene and SRY gene analysis. DHPLC method showed more sensitive than RFLP method for DNA fragments analysis. Therefore, DHPLC method can apply to identify for Hanwoo, Holstein and mixed beef.

• Journal of Gastric Cancer
• /
• v.6 no.4
• /
• pp.227-236
• /
• 2006

Purpose: Methylation of gene regulatory elements plays an important role in gene inactivation without genetic alteration. Gastric cancer is one of the tumors that exhibit a high frequency of CpG island hypermethylation. The purpose of this study was to investigate the occurrence of CpG island hypermethylation in gastric carcinoma in relation to H. pylori infection, CIMP and clincopathologic variables. Materials and Methods: We investigated the promoter methylation Status of six genes (hMLH1, p16, p14, COX-2, MGMT, E-cadherin) and CIMP in 36 gastric carcinoma tissues as well as in nontumor tissues. CIMP status was investigated by examining the methylation status of MINT 1, 2, 12, 25 and 31. The methylation status of the promoter was examined by methylation-specific PCR (MSP) and H. pylori infection was examined by histological diagnosis after staining with Warthin-Starry silver. Results: Among the 36 gastric carcinoma tissues, DNA hypermethylation was detected in the following frequencies: 14 (38.9%) for p14, 13 (36.1%) for p16, 8 (22.2%) for MGMT, 10 (27.8%) for COX-2, 21 (58.3%) for E-cadherin, and 6 (16.7%) for hMLH1. The frequencies for MINT1 and MINT25 hypermethylation were significantly higher in tumor tissues than in nontumor tissues. 16 (44.4%) of the 36 gastric carcinoma tissues were positive for the CIMP CIMP-H tumors were associated with older patients and larger tumor size than CIMP-L tumors. We found a significant association between the presence of the CIMP and hypermethylation of p16. Hypermethylation of p16 and MINT2 were significantly different when compared by age. MINT1 gene methylation was significantly associated with H. pylori infection (P=0.004). Conclusion: Our results suggest that aberrant hypermethylation of multiple tumor related genes (hMLH1, p16, p14, COX-2, MGMT, E-cadherin, MINT1, 2, 12, 25, 31) occurs frequently in gastric carcinoma tissues. The hypermethylation of MINT1 was significantly higher in the tumor tissues and was associated with H. pylori infection.

• Journal of Korean Society of Forest Science
• /
• v.112 no.2
• /
• pp.157-172
• /
• 2023

Controlled pollination (CP) is an important method in tree breeding programs because CP quickly generates desirable genotypes and rapidly maximizes genetic gains. However, few studies have evaluated the efficiency and success rate of CP in the breeding program of Pinus densiflora. To evaluate CP and the management of control pollinated progenies, we used 159 individuals in CB2 × KW40 or KW40 × CB2 populations that were established in 2015. After genotyping microsatellite loci, we estimated whether the number of primers was sufficient or not. Then, we performed pedigree analysis. The result showed that the number of primers was sufficient. By pedigree analysis, we found out that 60 of 159 individuals had been generated by the mating between CB2 and KW40. In the maternity analysis, there was evidence to indicate the possibility of management problems. Therefore, we excluded 54 individuals and repeated the pedigree analysis. In the second analysis, 47 of 105 individuals were generated by the mating between CB2 and KW40. To increase the efficiency of CP in tree breeding programs, several precautions are required. It is necessary to identify the exact clone names of the mother and father trees. In addition, CP processes should be performed properly, including deciding on the schedule of CP and the isolation of female strobili or flowers. Finally, the monitoring of hybrid progenies management after mating is important. Molecular markers should be used to identify the clone names of the mother and father trees and for monitoring post hoc management. This study provides a reference for tree breeding programs for the future control pollination of pine species.

• Korean Journal of Environmental Biology
• /
• v.41 no.4
• /
• pp.637-656
• /
• 2023

River estuaries are dynamic and productive ecosystems with high regional biodiversity. Environmental DNA (eDNA) has become a useful approach to assessing biodiversity in aquatic ecosystems. This study was conducted to investigate fish community characteristics and species diversity in two river estuary ecosystems, the Taehwa River and Changwon Stream. We further compared conventional and eDNA metabarcoding analyses of the fish communities. The conventional survey was performed in May, July, and October 2022, while the eDNA analysis was conducted only in May. We observed various fish species with different life histories, including carp, goby, and marine fish. We also found that migratory fish, such as dace Tribolodon hakonensis, sweetfish Plecoglossus altivelis, and eel Auguilla japonica, occurred in the Taehwa River, suggesting high river connectivity. Marine fish species were predominant in the Changwon Stream, as this river is located close to the sea. The diversity indices showed that the Taehwa River generally had higher species richness, evenness, and diversity values than the Changwon Stream. A total of 9-19 species were detected in the conventional survey for the three sites, whereas 11-18 species were found from eDNA analysis. The findings indicate that the sensitivity of eDNA was similar to or higher than that of the conventional method. Our study findings suggest the efficiency and efficacy of eDNA-based fish community monitoring, although with some shortcomings in applying the genetic marker to Korean fish, including no clear-cut distinction for Korean endemic species and/or genetically closely related species groups.