• Journal of Microbiology and Biotechnology
• /
• v.18 no.10
• /
• pp.1634-1640
• /
• 2008

This study was focused on the screening of valuable genetic resources, such as promoters from metagenome, and describes a promoter trapping system with a bidirectional probe concept, which can select promoters or operons from various biological resources including metagenomic DNA. A pair of reporters, GFP and DsRed, facing the opposite direction without promoters, is an effective system that can function regardless of the direction of inserted promoters. The feasibility of this system was tested for the isolation of constitutively expressed promoters in E. coli from a soil metagenome, resulting in a potential pool of various promoters for practical application. The analyses of structural organization of the trapped genes demonstrated that constitutively expressible promoters in E. coli were broadly distributed within the metagenome, and suggested that some promoters were useful for the construction of expression vectors. Based on these observations, three constitutive promoters were employed in the expression vector system and their potentials for practical application were evaluated in terms of expression level, protein solubility, and effects on host growth.

• Molecules and Cells
• /
• v.44 no.11
• /
• pp.843-850
• /
• 2021

The rapid increase in collateral omics and phenotypic data has enabled data-driven studies for the fast discovery of cancer targets and biomarkers. Thus, it is necessary to develop convenient tools for general oncologists and cancer scientists to carry out customized data mining without computational expertise. For this purpose, we developed innovative software that enables user-driven analyses assisted by knowledge-based smart systems. Publicly available data on mutations, gene expression, patient survival, immune score, drug screening and RNAi screening were integrated from the TCGA, GDSC, CCLE, NCI, and DepMap databases. The optimal selection of samples and other filtering options were guided by the smart function of the software for data mining and visualization on Kaplan-Meier plots, box plots and scatter plots of publication quality. We implemented unique algorithms for both data mining and visualization, thus simplifying and accelerating user-driven discovery activities on large multiomics datasets. The present Q-omics software program (v0.95) is available at http://qomics.sookmyung.ac.kr.

• Journal of the Computational Structural Engineering Institute of Korea
• /
• v.36 no.6
• /
• pp.391-398
• /
• 2023

In this paper, a penalized maximum likelihood estimation (PMLE) method that applies a penalty to increase the accuracy of a basis-screening-based Kriging model (BSKM) is introduced. The maximum order and set of basis functions used in the BSKM are determined according to their importance. In this regard, the cross-validation error (CVE) for the basis functions is employed as an indicator of importance. When constructing the Kriging model (KM), the maximum order of basis functions is determined, the importance of each basis function is evaluated according to the corresponding maximum order, and finally the optimal set of basis functions is determined. This optimal set is created by adding basis functions one by one in order of importance until the CVE of the KM is minimized. In this process, the KM must be generated repeatedly. Simultaneously, hyper-parameters representing correlations between datasets must be calculated through the maximum likelihood evaluation method. Given that the optimal set of basis functions depends on such hyper-parameters, it has a significant impact on the accuracy of the KM. The PMLE method is applied to accurately calculate hyper-parameters. It was confirmed that the accuracy of a BSKM can be improved by applying it to Branin-Hoo problem.

• Tuberculosis and Respiratory Diseases
• /
• v.69 no.3
• /
• pp.177-183
• /
• 2010

Background: Smoking reduces pulmonary function and induces various lung diseases. Recently, the rate of emphysema detection has increased due to lung cancer screening with low-dose chest computed tomography (CT). The purpose of this study was to evaluate changes in lung function associated with emphysema in healthy smokers. Methods: One hundred and ninety one healthy smokers, who had undergone a low-dose chest CT (LDCT) scan as part of lung cancer screening and had revisited the health center after a median 23.9 months' time, were recruited into this study. The severity of emphysema was calculated by the direct observation of a radiologist and a pulmonologist indipendently. Longitudinal changes in lung function according to emphysema based on LDCT and type of smoker was analyzed. Results: Of the participants in this study, 25% of healthy smokers had emphysema, which was mild in severity, in older patients (p=0.003) and in heavy smokers (p<0.001). $FEV_1/FVC$ and FEF25-75% were decreased in current smokers with emphysema (p=0.001 and p=0.009, respectively) and without emphysema (p=0.001 and p=0.042). Although lung function was not decreased in ex-smokers without emphysema, $FEV_1/FVC$ and FEF25-75% were decreased in ex-smoker with emphysema (p=0.020 and p=0.010). Conclusion: Upon examination with LDCT, the prevalence of emphysema was higher in healthy smokers was than in non-smokers. Lung function was diminished in smokers with emphysema, in spite of former smoker.

• Journal of Microbiology and Biotechnology
• /
• v.12 no.2
• /
• pp.286-291
• /
• 2002

Histone deacetylase I (HDAC1) works as one of the components in a nucleosome remodeling (NuRD) complex that consists of several proteins, including metastasis-associated protein 1 (MTA1). Since the protein-protein interaction of HDAC1 and MTA1 would appear to be important for both the integrity and functionality of the HDAC1 complex, the interruption of the HDAC1 and MTA1 interaction may be an efficient way to regulate the biological function of the HDAC1 complex. Based on this idea, a yeast two-hybrid system was constructed with HDAC1 and MTA1 expressing vectors in the DNA binding and activation domains, respectively. To verify the efficiency of the assay system, 3,500 microbial metabolite libraries were tested using the paper disc method, and KB0699 was found to inhibit the HDAC1 and MTA1 interaction without any toxicity to the wild-type yeast. Furthermore, KB0699 blocked the interaction of HDAC1 and MTA1 in an in vitro GST pull down assay and induced morphological changes in B16/BL6 melanoma cells, indicating the interruption of the HDAC1 complex function. Accordingly, these results demonstrated that the yeast assay strain developed in this study could be a valuable tool for the isolation of a HDAC1 complex disruptor.

• Journal of Microbiology and Biotechnology
• /
• v.14 no.5
• /
• pp.1067-1070
• /
• 2004

In the course of screening for specific inhibitors against the mycelial form of Candida albicans from natural resources, we have isolated and identified A6792-1 from Streptomyces sp. A6792 by using several chromatographies. By spectral analyses, this compound was determined as 7-oxostaurosporine, having a structure of staurosporine aglycon noiety. 7-Oxostaurosporine exhibited a selective growth inhibitory activity against the mycelial form of Candida spp. up to $100\mu\textrm{g}/disc$ in bioassay. It also exhibited a specific antifungal activity against the mycelial form of Candida spp. including C. krusei, C. albicans, C. tropicalis, and C. lusitaniae with MICs ranging from 3.1 to $25\mu\textrm{g}/ml$ 7-Oxostaurosporine demonstrated no in vivo toxicity in SPF ICR mice. Therefore, this compound may have a considerable potential as an antifungal agent based on the preferential inhibition against growth of the mycelial form of Candida spp., dimorphic fungi.

• Proceedings of the Korean Institute of Surface Engineering Conference
• /
• 2017.05a
• /
• pp.169-169
• /
• 2017

Due to key roles for the electrochemical stability and charge capacity the solid-electrolyte interphase (SEI) has been extensively studied in anodes of a Li-ion battery cell. There is, however, few of investigation for cathodes. Using first-principles based calculations we describe atomic-level process of the SEI layer formation at the interface of a carbonate electrolyte and $LiMn_2O_4$ spinel cathode. Furthermore, using beyond the conventional density functional theory (DFT+U) calculations we examine the work function of the cathode and frontier orbitals of the electrolyte. Based on the results we propose that proton transfer at the interface is an essential mechanism initiating the SEI layer formation in the $LiMn_2O_4$. Our results can guide a design concept for stable and high capacity Li-ion battery cell through screening an optimum electrolyte fine-tuned energy band alignment for a given cathode.

• Journal of Integrative Natural Science
• /
• v.9 no.1
• /
• pp.41-61
• /
• 2016

Non-small cell lung cancer (NSCLC) is the leading cause of cancer-related mortality worldwide. Phosphoinositide 3-kinases (PI3Ks) play important role in Non-Small Cell Lung Cancer. PI3Ks constitute a lipid kinase family which modulates the function of numerous substrates involved in the regulation of cell survival, cell cycle progression and cellular growth. Herein, we describe the ligand based pharmacophore combined with molecular docking studies methods to identify new potent PI3K inhibitors. Several pharmacophore models were generated and validated by Guner-Henry scoring Method. The best models were utilized as 3D pharmacophore query to screen against ZINC database (Chemical and Natural) and the retrieved hits were further validated by fitness score, Lipinski's rule of five. Finally four compounds were found to have good potential and they may act as novel lead compounds for PI3K inhibitor designing.

• Therapeutic Science for Rehabilitation
• /
• v.8 no.3
• /
• pp.43-55
• /
• 2019

Objective: The purpose of this study is to conduct a preliminary research for the development of a Performance-Based Cognitive Function Test (PCFT) to screen the elderly for cognitive function impairment, and examine the reliability and validity of the test. Methods: A draft version of the Performance-Based Cognitive Function Test (PCFT) was developed and utilized in nine healthy elderly individuals. In order to verify its reliability, we analyzed the internal consistency of the PCFT. In order to verify the concurrent validity of the PCFT, this study analyzed the correlation between motor-cognitive dual task assessments and the Korean version of the Mini-Mental State Examination (MMSE-K). Results: The internal consistency of the PCFT for motor and cognitive tasks was 0.871 and 0.959 (Cronbach's ${\alpha}$), respectively. Concurrent validity of the PCFT, which was performed through motor-cognitive dual task assessments, ranged from 0.755 to 0.964 (Spearman's rho statistic, p < 0.05). In addition, correlation between the cognitive assessment tool and the MMSE-K ranged from 0.849 to 0.943 (p < 0.01). Conclusion: This study verified, and established the reliability and validity of the PCFT. Further studies are required to examine other psychometric properties in a modified PCFT, for screening cognitive function impairments in the elderly.

• Journal of The Korean Society of Integrative Medicine
• /
• v.7 no.3
• /
• pp.51-59
• /
• 2019

Purpose : To evaluate the effect of comprehensive art therapy on physical function and activities of daily living in children with cerebral palsy (CP). Methods : Ten ambulant children with diplegic (n=8) or hemiplegic (n=2) CP participated in this study. All were randomly assigned to either the art therapy group (n=5) or the control group (n=5). Both groups received physical therapy based on neurodevelopmental techniques for 20 minutes a day, 1 day a week, for a period of 12 weeks. Children in the art therapy group received additional comprehensive art therapy for 70 minutes once a week for 3 months. Tests for various measurements-Motricity Index (MI) for strength, Trunk Control Test (TCT) for trunk ability, Gross Motor Function Measure (GMFM) and Gross Motor Function Classification System (GMFCS) for gross motor function, Denver Developmental Screening Test-II (DDST-II) for developmental milestones, Functional Independence Measure of Children (WeeFIM) for abilities to complete daily activities, Leg and Hand Ability Test (LHAT) for limb function-were performed before and after treatments. Results : The upper extremity and whole extremity strengths of MI, self-care and total scores of WeeFIM, and leg and arm functions of LHAT improved significantly only for individuals in the art therapy group after the art therapy (p<.05). The value of MI after treatment was at the upper extremity and whole extremity strengths the leg function of LHAT was also significantly improved compared to the control group (p<.05). Conclusion : This study revealed that comprehensive art therapy along with physiotherapy was effective in increasing upper extremity strength and leg ability in children with CP. This suggests that comprehensive art therapy may be a useful adjunctive therapy for children with CP.