• The Journal of the Korea Contents Association
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• v.14 no.11
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• pp.541-548
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• 2014

In this paper, we introduce a second version of modified binary particle swarm optimization using a concept of genotype-phenotype in genetic algorithms. Particle swarm optimization uses an information of difference between a position of the best solution and one's own position in the process of searching optimum. To obtain this difference of positions, the first version of modified binary particle swarm optimization uses a phenotype but the proposed second version uses a genotype. We can represent the solution space in large search space by using a genotype which provides continuous whole space as search space compared to a phenotype which provides only binary information. Experimental results in 10 De Jong benchmark function show that the second version outperforms the first version in six functions which has a broad search space and many local optima.

• Genomics & Informatics
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• v.12 no.4
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• pp.289-292
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• 2014

Next-generation sequencing (NGS) is widely used to identify the causative mutations underlying diverse human diseases, including cancers, which can be useful for discovering the diagnostic and therapeutic targets. Currently, a number of single-nucleotide variant (SNV)-calling algorithms are available; however, there is no tool for visualizing the recurrent and phenotype-specific mutations for general researchers. In this study, in order to support defining the recurrent mutations or phenotype-specific mutations from NGS data of a group of cancers with diverse phenotypes, we aimed to develop a user-friendly tool, named mutation arranger for defining phenotype-related SNV (MAP). MAP is a user-friendly program with multiple functions that supports the determination of recurrent or phenotype-specific mutations and provides graphic illustration images to the users. Its operation environment, the Microsoft Windows environment, enables more researchers who cannot operate Linux to define clinically meaningful mutations with NGS data from cancer cohorts.

• Proceedings of the Korean Society of Toxicology Conference
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• 2001.10a
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• pp.156-156
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• 2001

We have previously shown that H-ras, but N-ras, induces an invasiveness and cell motility in human breast epithelial cells (MCFl0A), while both H-ras and N-ras induce transformed phenotype. It has been recently shown that phosphatidylinositol 3-kinase (PI3K) plays an important role on cell migration. In the present study, we wished to investigate the functional role of PI3K in H-ras-induced invasive phenotype in MCF10A cells.(omitted)

• Journal of Microbiology and Biotechnology
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• v.1 no.3
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• pp.169-175
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• 1991

Pediococcus acidilactici strain M produced a bacteriocin which was proteinaceous, heat stable, and exhibited antimicrobial activity against lactic acid bacteria, variety of food spoilage and pathogenic bacteria. The antimicrobial activity was not caused by $H_2$$O_2$ and organic acid, and was remained between pHs of 4.0 to 9. Molecular weight of crude bacteriocin was approximately 2, 500. Phenotypic assignment after plasmid cruing experiment demonstrated that a 53.7 kilobase (kb) plasmid, designated as pSUC53, was responsible for the sucrose fermentation phenotype ($Suc^+$) and a 11.1 kb plasmid, designated as pBAC11, was associated with bacteriocin production phenotype ($Bac^+$). Neither of the two plasmids were linked to antibiotic resistance.

• Nutrition Research and Practice
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• v.6 no.2
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• pp.120-125
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• 2012

The aim of this study was to investigate the influencing factors that characterize low density lipoprotein (LDL) phenotype and the levels of LDL particle size in healthy Korean women. In 57 healthy Korean women (mean age, $57.4{\pm}13.1$ yrs), anthropometric and biochemical parameters such as lipid profiles and LDL particle size were measured. Dietary intake was estimated by a developed semi-quantitative food frequency questionnaire. The study subjects were divided into two groups: LDL phenotype A (mean size: $269.7{\AA}$, n = 44) and LDL phenotype B (mean size: $248.2{\AA}$, n = 13). Basic characteristics were not significantly different between the two groups. The phenotype B group had a higher body mass index, higher serum levels of triglyceride, total-cholesterol, LDL-cholesterol, apolipoprotein (apo)B, and apoCIII but lower levels of high density lipoprotein (HDL)-cholesterol and LDL particle size than those of the phenotype A group. LDL particle size was negatively correlated with serum levels of triglyceride (r = -0.732, $P$ < 0.001), total-cholesterol, apoB, and apoCIII, as well as carbohydrate intake (%En) and positively correlated with serum levels of HDL-cholesterol and ApoA1 and fat intake (%En). A stepwise multiple linear regression analysis revealed that carbohydrate intake (%En) and serum triglyceride levels were the primary factors influencing LDL particle size ($P$ < 0.001, $R^2$ = 0.577). This result confirmed that LDL particle size was closely correlated with circulating triglycerides and demonstrated that particle size is significantly associated with dietary carbohydrate in Korean women.

• Korean Journal of Clinical Laboratory Science
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• v.55 no.2
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• pp.113-120
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• 2023

The hypertriglyceridemic-waist (HTGW) phenotype can predict the risk of coronary artery disease. This study evaluated the relationship between the HTGW phenotype and metabolic abnormalities in hypertensive adults. The test was conducted on adult hypertension patients aged 20 or older who underwent health checkups from January 2018 to December 2021 at general hospitals in Gyeonggi Province. The HTGW phenotype was triglyceride ≥150 mg/dL and waist circumference ≥90 cm for men and ≥85 cm for women. The prevalence of the HTGW phenotype in the study subjects was 17.9%. After adjusting for age, gender, and BMI, the odds ratio of the HTGW group was 5.09 (95% confidence interval [CI]: 3.545~7.309) for low HDL-cholesterol, 1.68 (95% CI: 1.176~2.411) for high LDL-cholesterol, was 2.92 (95% CI: 2.009~4.235) for high total cholesterol, 3.39 (95% CI: 2.124~5.412) for diabetes and 1.85 (95% CI: 1.286~2.674) for hyperuricemia compared to the normal triglyceride levels with the normal waist (NTNW) group. The area under curve values of the HTGW phenotype for diagnosing metabolic syndrome were 0.849 for all subjects, 0.858 for men, and 0.890 for women. In conclusion, the HTGW phenotype is closely related to metabolic abnormalities and is a useful indicator for monitoring adult hypertensive patients with metabolic syndrome.

• Proceedings of the Korean Society of Crop Science Conference
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• 2022.10a
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• pp.290-290
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• 2022

Powdery mildew is known to be one of the serious diseases in C. moschata cultivation. Plants infected with powdery mildew cause damage to cultivation areas such as occurrence of deformity fruit and decrease in quantity. also, it has been reported that many farms have difficulties in controlling powdery mildew due to the outbreak under various conditions throughout the year. Therefore, this study intends to perform a phenotype test and a genotype test for C. moschata 60 lines grown in Jenong S&T. Podospareaxanthii, known as a pathogen that causes powder mildew disease in pumpkins in Korea, was collected and used as an inoculation source, phenotype test was performed by examining the infection area rate(%) of powdery mildew disease that occurred in leaves 25 days after inoculation. It was determined that 0% of the infection area rate was in the first stage, 1 to 5% in the second stage, 6 to 15% in the third stage, 16 to 30% in the fourth stage, and 31% or more in the fifth stage, The first and second stages were judged as resistance, the third as moderate resistance, and the fourth and fifth stages as sensitivity. As a result of the phenotype test, it was confirmed that the resistance was 21 points, moderate resistance was 14 points, and sensitivity was 25 points. After searching for the genes related to powdery mildew resistance resistance, pm-0, CmbHLH87, and LOC111453072, 21 points of resistance and 9 points of moderate resistance identified through phenotype tests were identified through gel electrophoresis after polymerase chain reaction(PCR) using 5 primers related to 3 genes. As a result of genotype testing of a total 30 points, the CmbHLH87 and LOC111453072 gene were found to be resistant bands in all points, PMR1 was identified as 20 points for resistance, 4 points for moderate resistance, and 6 points for sensitivity, PMR2 was not identified in the entire band, and PMR5 was identified as 18 point for resistance, 3 points for moderate resistance, and 9 points for sensitivity. As a result, when comparing the phenotype test results and genotype test results, CmbHLH87 and LOC111453072 genes was 100% consistent in resistance and moderate resistance, PMR1 was 95.2% in resistance, 44.4% in moderate resistance, and PMR5 was 90% in resistance and 33.3% in moderate resistance, PMR2 was not consistent in resistance and moderate resistance. Therefore, it is expected that more accurate PMR test will be possible by using molecular markers(PMR1, PMR5) and by developing CmbHLH87 and LOC111453072 gene-related molecular markers.

• BMB Reports
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• v.43 no.2
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• pp.79-90
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• 2010

Mouse models are crucial for the functional annotation of human genome. Gene modification techniques including gene targeting and gene trap in mouse have provided powerful tools in the form of genetically engineered mice (GEM) for understanding the molecular pathogenesis of human diseases. Several international consortium and programs are under way to deliver mutations in every gene in mouse genome. The information from studying these GEM can be shared through international collaboration. However, there are many limitations in utility because not all human genes are knocked out in mouse and they are not yet phenotypically characterized by standardized ways which is required for sharing and evaluating data from GEM. The recent improvement in mouse genetics has now moved the bottleneck in mouse functional genomics from the production of GEM to the systematic mouse phenotype analysis of GEM. Enhanced, reproducible and comprehensive mouse phenotype analysis has thus emerged as a prerequisite for effectively engaging the phenotyping bottleneck. In this review, current information on systematic mouse phenotype analysis and an issue-oriented perspective will be provided.

• The Plant Pathology Journal
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• v.27 no.2
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• pp.128-137
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• 2011

Fifty two Macrophomina phaseolina isolates were recovered from 24 host plant species through the 14 Iranian provinces. All isolates were confirmed to species using species-specific primers. The colony characteristics of each isolate were recorded, including chlorate phenotype, relative growth rate at $30^{\circ}C$ and $37^{\circ}C$, average size of microsclerotia, and time to microsclerotia formation. The feathery colony phenotype was the most common (63.7%) on the chlorate selective medium and represented the chlorate sensitive phenotype of the Iranian Macrophomina phaseolina population. Meantime, inter simple sequence repeats (ISSR) Markers were used to assess the genetic diversity of the fungus. Unweighted pair-group method using arithmetic means (UPGMA) clustering of data showed that isolates did not clearly differentiate to the specific group according to the host or geographical origins, however, usually the isolates from the same host or the same geographic origin tend to group nearly. Our results did not show a correlation between the genetic diversity based on the ISSR and phenotypic characteristics. Similar to the M. phaseolina populations in the other countries, the Iranian isolates were highly diverse based on the phenotypic and the genotypic characteristics investigated and needs more studies using neutral molecular tools to get a deeper insight into this complex species.

• Journal of Pharmacopuncture
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• v.22 no.4
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• pp.253-259
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• 2019

Objectives: It is reported that tumor-associated macrophages (TAMs) contribute to cancer progression by promoting tumor growth and metastasis. The purpose of this study is to investigate the effect of different fractions of Adenophora triphylla var. japonica (AT) on the polarization of macrophages into the M2 phenotype, a major phenotype of TAMs. Methods: We isolated hexane, ethyl acetate, and butanol fractions from crude ethanol extract of AT. The cytotoxicity of AT in RAW264.7 cells was examined by 3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay. RAW264.7 cells were polarized into the M2 phenotype by treatment with interleukin (IL)-4 and IL-13. The expression of M2 macrophage marker genes was detected by reverse transcription polymerase chain reaction (RT-PCR). The phosphorylation level of signal transducer and activator of transcription 6 (STAT6) was investigated by western blot analysis. The migration of Lewis lung carcinoma (LLC) cells was examined by transwell migration assay using conditioned media (CM) collected from RAW264.7 cells as a chemoattractant. Results: Among various fractions of AT, the ethyl acetate fraction of AT (EAT) showed the most significant suppressive effect on the mRNA expression of M2 macrophage markers, including arginase-1, interleukin (IL)-10 and mannose receptor C type 1 (MRC-1), up-regulated by treatment of IL-4 and IL-13. In addition, EAT suppressed the phosphorylation of STAT6, a critical regulator of IL-4 and IL-13-induced M2 macrophage polarization. Finally, the increased migration of Lewis lung carcinoma (LLC) cells by CM from M2-polarized RAW264.7 cells was reduced by CM from RAW264.7 cells co-treated with EAT and M2 polarization inducers. Conclusion: We demonstrated that EAT attenuated cancer cell migration through suppression of macrophage polarization toward the M2 phenotype. Additional preclinical or clinical researches are needed to evaluate its regulatory effects on macrophage polarization and anti-cancer activities.