• Asian Pacific Journal of Cancer Prevention
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• v.14 no.8
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• pp.4621-4625
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• 2013

The purpose of this study was to construct a protein-protein interaction (PPI) network related to oral squamous cell carcinoma (OSCC). Each protein was ranked and those most associated with OSCC were mined within the network. First, OSCC-related genes were retrieved from the Online Mendelian Inheritance in Man (OMIM) database. Then they were mapped to their protein identifiers and a seed set of proteins was built. The seed proteins were expanded using the nearest neighbor expansion method to construct a PPI network through the Online Predicated Human Interaction Database (OPHID). The network was verified to be statistically significant, the score of each protein was evaluated by algorithm, then the OSCC-related proteins were ranked. 38 OSCC related seed proteins were expanded to 750 protein pairs. A protein-protein interaction nerwork was then constructed and the 30 top-ranked proteins listed. The four highest-scoring seed proteins were SMAD4, CTNNB1, HRAS, NOTCH1, and four non-seed proteins P53, EP300, SMAD3, SRC were mined using the nearest neighbor expansion method. The methods shown here may facilitate the discovery of important OSCC proteins and guide medical researchers in further pertinent studies.

• Asian Pacific Journal of Cancer Prevention
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• v.13 no.5
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• pp.1833-1836
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• 2012

Objective: Promoter methylation, which can be regulated by MTHFR activity, is associated with silencing of genes. In this study we evaluated the methylation status (type) of the BRCA2 promoter in ovarian cancer patients carrying different genotypes of the MTHFR gene (A or C polymorphisms at position 1298). Methods: The methylation type of the BRCA2 promoter was evaluated using bisulfate-modified DNA in methylation-specific PCR and the MTHFRa1278c polymorphism was assessed by PCR-RFLP. Results: Analysis of the BRCA2 promoter methylation type of cases showed that 7 out of 60 cases (11.7%) were methylated while the remaining 53 (88.3%) were unmethylated. In methylated cases, one out of the 7 cases had a CC genotype and the remaining 6 methylated cases had an AC genotype. The AA genotype was absent. In unmethylated cases, 34, 18, and one out of these had AC, AA and CC genotype, respectively. Conclusion: There was no significant relationship between the methylation types of the BRCA2 promoter in different genotypes of MTHFRa1298c polymorphism in ovarian cancer; p=0.255. There was no significant relation between the methylation types of the BRCA2 promoter in different genotypes of the MTHFRa1298c polymorphism in ovarian cancer.

• Korean Journal of Fisheries and Aquatic Sciences
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• v.53 no.4
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• pp.492-498
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• 2020

Despite its economic importance, olive flounder Paralichthys olivaceus aquaculture industry is facing a crisis with a continuous production decline. There have been many solutions to overcome the complicate predicament proposed. Increasing genetic diversity and discovering new commercial value through selective breeding are among them. The aims of the present study are to increase the selection power of the golden flounders. We examined the genetic diversity of the breeder population of golden flounders and developed selective markers for the golden flounder population. The 6 microsatellite (MS) markers were selected from melanogenesis-related genes, which are believed to be involved in the pigmentation of fish. All markers were polymorphic (except PO4) and 5 of them had PIC value of 0.6 or above. All makers had distinctive alleles indicating either normal or golden individuals. For examples, from PO4 marker, the frequency of an allele (316) in the golden population was 100% and in normal population was 0% (P<0.001). Although some more studies with more samples at the later generations should be performed to confirm this result, the 316 allele from PO4 marker could be a distinctive tool for decision of the colors in olive flounders at an early stage of the life cycle.

• The Plant Pathology Journal
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• v.38 no.1
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• pp.1-11
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• 2022

Fusarium culmorum is one of the most important causal agents of root rot of wheat. In this study, 10 F. culmorum isolates were collected from farms located in five agro-ecological regions of Morocco. These were used to challenge 20 durum wheat genotypes via artificial inoculation of plant roots under controlled conditions. The isolate virulence was determined by three traits (roots browning index, stem browning index, and severity of root rot). An alpha-lattice design with three replicates was used, and the resulting ANOVA revealed a significant (P < 0.01) effect of isolate (I), genotype (G), and G × I interaction. A total of four response types were observed (R, MR, MS, and S) revealing that different genes in both the pathogen and the host were activated in 53% of interactions. Most genotypes were susceptible to eight or more isolates, while the Moroccan cultivar Marouan was reported resistant to three isolates and moderately resistant to three others. Similarly, the Australian breeding line SSD1479-117 was reported resistant to two isolates and moderately resistant to four others. The ICARDA elites Icaverve, Berghisyr, Berghisyr2, Amina, and Icaverve2 were identified as moderately resistant. Principal component analysis based on the genotypes responses defined two major clusters and two sub-clusters for the 10 F. culmorum isolates. Isolate Fc9 collected in Khemis Zemamra was the most virulent while isolate Fc3 collected in Haj-Kaddour was the least virulent. This work provides initial results for the discovery of differential reactions between the durum lines and isolates and the identification of novel sources of resistance.

• Journal of Genetic Medicine
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• v.19 no.2
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• pp.85-93
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• 2022

Purpose: Cornelia de Lange syndrome (CdLS) is a rare genetically heterogeneous disorder caused by genetic variants of the cohesin complex. However, the diverse genetic etiologies and their phenotypic correlations in Korean patients with CdLS are still largely unknown. Hence, this study aimed to clarify the clinical characteristics and genetic background of Korean patients with CdLS. Materials and Methods: The medical records of 15 unrelated patients (3 males and 12 females) genetically confirmed to have CdLS were retrospectively reviewed. All individuals were diagnosed with CdLS using target gene analysis, whole-exome sequencing, and/or chromosomal microarray analysis. The clinical score (CS) was calculated to assess disease severity. Results: The median age at diagnosis was 1.7 (range, 0.0-11.8) years, and median follow-up duration was 3.8 (range, 0.4-11.7) years. Eight (53.3%) patients showed classic phenotypes of CdLS, two (13.3%) showed non-classic phenotypes, and five (33.3%) had other phenotypes sharing limited signs of CdLS. Fifteen causative variants were identified: NIPBL in five (33.3%, including 3 males), SMC1A in three (20.0%), SMC3 in three (20.0%), and HDAC8 in four (26.7%) patients. The CS was significantly higher in the NIPBL group than in the non-NIPBL group (14.2±1.3 vs. 8.7±2.9, P<0.001). Conclusion: We identified the clinical and genetic heterogeneity of CdLS in Korean patients. Patients with variants of NIPBL had a more distinctive phenotype than those carrying variants of other cohesin complex genes (SMC1A, SMC3, and HDAC8). However, further studies are warranted to understand the pathogenesis of CdLS as a cohesinopathy and its genotype-phenotype correlations.

• Journal of Korean Society of Forest Science
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• v.77 no.4
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• pp.382-388
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• 1988

Improvement of productivity by forest tree breeding work in Korea was estimated for a few important tree species. Progenies of 17 plus trees of red pine (Pines densiflora) outgrew by 57 percentage compared with progenies of unselected trees at age 15. If best three families are selected among the 17, more than double in volume grow-th is expected. The hybrid Pinus rigida ${\times}$ P. taeda showed more than double volume growth compare to P. rigida at a southern plantation at age 15. However, the superiority of the hybrid decreased at northern plantations, mainly because of low coldhardiness of the hybrid. At a northern plantation, the hybrid grew less than the P. rigida on upper hill, while the hybrid grew much better than the P. rigida on flat area. Another hybrid Populus alba ${\times}$ P. glandulosa grew faster than both parents by two to two and half times according to planting sites at age 10. Introduction of Pinus rigida also showed increased volume growth. Volume increase by selection of best five provenances among 45 at age 12 was estimated as 53 percent compare to progenies of plus trees in Korea, Additional 19 percent of volume increase was expected by selection of the best families within the best provenances. Annual production of chestnuts reached about 70,000 M/T by planting resistant clones to chestnut gall wasp (Dryocosmus kuriphilus), which killed almost all susceptible trees. Although polyploid trees and mutants have been produced by colchicine treatments in over 10 tree species, none of them is economically important Remarkable improvement of productivity is expected by biotechnology in future through selection, hybridization, introduction of foreign genes at cell, cell organelle and gene level, and gene transformation. At present, mass propagation of superior planting materials by tissue culture will increase the productivity.

• Journal of the Korean Society of Food Science and Nutrition
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• v.42 no.11
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• pp.1717-1726
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• 2013

Fermentation characteristics and health functionalities of kimchi by inoculating kimchi lactic acid bacteria (LAB) starters were studied. We manufactured single LAB starter kimchi (Lactobacillus plantarum pnuK, Lactobacillus plantarum 3099K, Leuconostoc mesenteroides pnuK), mixed LAB starter kimchi (Lb. plantarum pnu/Leu. mesenteroides pnuK, Lb. plantarum 3099/Leu. mesenteroides pnuK) with inoculum size of $10^6$ CFU/g, as well as naturally fermented kimchi (NK), and fermented them for 6 days at $15^{\circ}C$. The pH and acidity of the early phase of fermentation were not different, but kimchi with the starters showed rapid changes in the pH and acidity from 2 days of fermentation. As the fermentation progressed, the level of total aerobic bacteria and Lactobacillus sp. increased similarly with or without Lb. plantarum (LP) inoculation. However, the level of Leuconostoc sp. was high in kimchi inoculated with Leuconostoc sp. starter. In the sensory evaluation test, kimchi with starters received higher overall acceptability scores than those of NK; mixed starter added kimchi earned the highest score. In DPPH and hydroxyl radical scavenging activity, kimchi with the starters exhibited higher activity than that of NK. In the MTT assay of HCT-116 and HT-29 human colon cancer cells, NK showed inhibition rates of 63.4 and 51.9%, but LPpnuK achieved 77.1 and 68.8%, respectively. This study showed that inoculating starters in kimchi increased in vitro antioxidant and anticancer activities, and single starter (LP) added kimchi revealed higher functionality than the kimchi with mixed starter. Kimchis with the starters effectively up-regulated the gene expressions of the pro-apoptotic gene of Bax, but down-regulated Bcl-2. They promoted expressions of p53 and p21, and suppressed expressions of inflammation-related genes, iNOS and COX-2, compared with NK. Taken together, it is expected that using starters may help manufacture kimchi with improved sensory quality and health functionality.

• Journal of Physiology & Pathology in Korean Medicine
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• v.17 no.4
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• pp.914-922
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• 2003

Ailanthus altissima has been used to settle an upset stomach, to alleviate a fever, and as an insecticide. We reported that the water extract of A. altissima induced apoptotic cell death in HL-60 human leukemia cell line. Here, we showed the dose-dependent inhibitions of cell viability by the extract, as measured by cell morphology. The cell cycle control genes are considered to play important roles in tumorigenesis. The purpose of the present study is also to investigate the effect of A. altissima on cell cycle progression and its molecular mechanism in the cells. The level of p21 protein was increased after treatment of the extract, whereas both Bcl-2 and Bax protein levels were not changed. These results suggest that A. altissima induces apoptotic cell death via p21-dependent signaling pathway in HL-60 human leukemia cell line which delete wild type p53. G1 checkpoin related gene products tested (cyclin D3, cyclin dependent kinase 4, retinoblastoma, E2F1) were decreased in their protein levels in a dose-dependent manner after treatment of the extract. Taken together, these results indicate that the increase of apoptotic cell death by A. altissima may be due to the inhibition of cell cycle in HL-60 human leukemia cell line

• Journal of Ginseng Research
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• v.45 no.2
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• pp.316-324
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• 2021

Background: Korea Red Ginseng (KRG) has been used as remedies with hepato-protective effects in liver-related condition. Microbiota related gut-liver axis plays key roles in the pathogenesis of chronic liver disease. We evaluated the effect of KRG on gut-liver axis in patients with nonalcoholic statohepatitis by the modulation of gut-microbiota. Methods: A total of 94 patients (KRG: 45 and placebo: 49) were prospectively randomized to receive KRG (2,000 mg/day, ginsenoside Rg1+Rb1+Rg3 4.5mg/g) or placebo during 30 days. Liver function test, cytokeraton 18, and fatigue score were measured. Gut microbiota was analyzed by MiSeq systems based on 16S rRNA genes. Results: In KRG group, the mean levels (before vs. after) of aspartate aminotransferase (53 ± 19 vs. 45 ± 23 IU/L), alanine aminotransferase (75 ± 40 vs. 64 ± 39 IU/L) and fatigue score (33 ± 13 vs. 26 ± 13) were improved (p < 0.05). In placebo group, only fatigue score (34 ± 13 vs. 31 ± 15) was ameliorated (p < 0.05). The changes of phyla were not statistically significant on both groups. In KRG group, increased abundance of Lactobacillus was related with improved alanine aminotransferase level and increased abundance of Clostridium and Intestinibacter was associated with no improvement after KRG supplementation. In placebo group, increased abundance of Lachnospiraceae could be related with aggravation of liver enzyme (p < 0.05). Conclusion: KRG effectively improved liver enzymes and fatigue score by modulating gut-microbiota in patients with fatty liver disease. Further studies are needed to understand the mechanism of improvement of nonalcoholic steatohepatitis. ClnicalTrials.gov: NCT03945123 (www.ClinicalTrials.gov).

• Clinical and Experimental Pediatrics
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• v.53 no.4
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• pp.548-553
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• 2010

Purpose : IgA nephropathy (IgAN) is the most commonly occurring form of chronic glomerulonephritis in pediatric cases. Human leukocyte antigen (HLA) genes have been implicated in various inflammatory and autoimmune diseases. The present study was conducted to investigate the association between 2 single nucleotide polymorphisms (SNPs) of the HLA-G gene and childhood IgAN. Methods : The authors analyzed and compared $HLA-G$ gene SNPs (rs1736936 and rs2735022) in 174 patients with childhood IgAN and in 438 healthy controls. In addition, IgAN patients were dichotomized and compared with respect to proteinuria (< and >$4mg/m^2/hour$), the presence or absence of podocyte foot process effacement, and the presence of pathologically early and advanced disease markers such as interstitial fibrosis, tubular atrophy, or global sclerosis. Results : No significant SNP frequency differences were observed for the $HLA-G$ gene between IgAN patients and the control group. Moreover, no significantly associated SNP was observed with the presence of proteinuria, podocyte foot process effacement, or pathologically advanced markers. However, the haplotype, composed of rs1736936 and rs2735022, showed a significant association with the susceptibility to develop childhood IgAN (haplotype T/C: dominant model, $P$=0.049; haplotype C/T: recessive model, $P$=0.030). Conclusion : Our results indicate that rs1736936 and rs2735022 as the $HLA-G$ gene promoter haplotype might be associated with the susceptibility to develop childhood IgAN in the Korean population.