• Interdisciplinary Bio Central
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• v.2 no.2
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• pp.6.1-6.5
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• 2010

Fragment molecular orbital (FMO) method provides a novel tool for ab initio calculations of large biomolecules. This method overcomes the size limitation difficulties in conventional molecular orbital methods and has several advantages compared to classical force field approaches. While there are many features in this method, we here focus on explaining the issues related to protein-ligand binding: FMO method provides useful interaction-analysis tools such as IFIE, CAFI and FILM. FMO calculations can provide not only binding energies, which are well correlated with experimental binding affinity, but also QSAR descriptors. In addition, FMO-derived charges improve the descriptions of electrostatic properties and the correlations between docking scores and experimental binding affinities. These calculations can be performed by the ABINIT-MPX program and the calculation results can be visualized by its proper BioStation Viewer. The acceleration of FMO calculations on various computer facilities is ongoing, and we are also developing methods to deal with cytochrome P450, which belongs to the family of drug metabolic enzymes.

• Proceedings of the Korean Society of Toxicology Conference
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• 2001.10a
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• pp.195-195
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• 2001

The inhibitory potentials of TCAs (imipramine, desipramine, amitriptyline, and nortriptyline) on phenytoin p-hydroxylation and probe metabolic pathways of each CYP isoforms were evaluated from incubation studies of human liver microsomes and cDNA-expressed cytochrome P450s in vitro in order to understand the mechanism of drug interaction between TCAs and phenytoin, a substrate of CYP2C9 and CYP2C19. (omitted)

• Journal of Plant Biotechnology
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• v.40 no.3
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• pp.111-124
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• 2013

Research on the basic interaction of radiation with biological systems has contributed to human society through various applications in pharmaceutical, medicine, agriculture and other technological developments. In the agricultural sciences and food technology sectors, the last few decades have witnessed a large number of pertinent works regarding the utilization of radiation for evolution of superior varieties of agricultural crops of economic importance. This review presents general information about the effect of radiation on plant specificity, dose response, and benefits. There has been summarized of the effects observed after exposure and influenced by several factors including plant characteristics and radiation features. We also report on the effect of ${\gamma}$-irradiations on plants, focusing on metabolic alterations, modifications of growth and development and changes in biochemical pathways.

• Molecules and Cells
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• v.25 no.3
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• pp.452-456
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• 2008

The interactions between monocytes and extracellular matrix proteins have been implicated in atherosclerosis pathophysiology. In the present study we evaluated monocyte attachment and migration through oxidized and non-oxidized collagen IV. Monocyte attachment was tested on microwells coated with either native or oxidized collagen IV. Monocyte migration through collagen IV was examined on transwells. Monocytes derived from patients with diabetes mellitus showed an increased ability to attach and migrate through collagen IV as compared to those derived from healthy volunteers. Moreover, control monocytes attached to oxidized collagen at a higher degree, while they migrated through oxidized collagen at a lower degree, as compared to the native protein. Our results also showed the involvement of the alpha2 integrin subunit in the above phenomena suggesting a modified interaction between monocytes and collagen IV in diabetes mellitus.

• Journal of Pharmaceutical Investigation
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• v.41 no.3
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• pp.143-146
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• 2011

Scutellariae Radix is widely used in the traditional herbal medicine for the treatment of fever, cough, dysentery, hepatitis and hypertension in Korea, China and Japan. In this study, we investigated the effects of 70% ethanolic extract of Scutellariae Radix (SRE) on CYP450-mediated drug metabolism in the in vitro systems using human liver microsomes and hepatocytes. The microsomal incubation assay showed that SRE inhibited the drug metabolism reactions catalyzed by CYP1A2, CYP2C8 and CYP2C9 in a dose-dependent manner. In particular, SRE was shown to strongly inhibit the metabolic activity of CYP1A2 with an $IC_{50}$ value of 4.6 ${\mu}g/mL$. When SRE was evaluated for its effect on the induction of CYP450 enzyme activities in cryopreserved human hepatocytes, SRE did not exhibit any effect.

• PNF and Movement
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• v.6 no.1
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• pp.41-51
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• 2008

Purpose : This paper reviews evidence supporting adaptive plasticity in skeletal muscle fibers induced by various exercise training and neuromuscular activity. Result : Skeletal muscle fiber demonstrates a remarkable adaptability and can adjust its physiologic and contractile makeup in response to alterations in functional demands. This adaptive plasticity results from the ability of muscle fibers to adjust their molecular, functional, and contractile properties in response to altered physiological demands, such as changes in exercise patterns and mechanical loading. The process of activity-dependent plasticity in skeletal muscle involves a multitude of signalling mechanisms initiating replication of specific genetic sequences, enabling subsequent translation of the genetic message and ultimately generating a series of myosin heavy chain isoform. Conclusions : Knowledge of the mechanisms and interaction of activity-dependent adaptive pathways in skeletal muscle is important for our understanding of the synthesis of muscle myosin protein, maintenance of metabolic and functional capacity with physical activity, and therapeutic intervention for functional improvement.

• Journal of Microbiology and Biotechnology
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• v.25 no.8
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• pp.1181-1194
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• 2015

Tuberculosis (TB) is an infectious disease transmitted by aerosol droplets and characterized by forming granulomatous lesions. Although the number of people infected in the population is high, the vast majority does not exhibit symptoms of active disease and only 5-10% develop the disease after a latent period that can vary from weeks to years. The bases of the immune response for this resistance are unknown, but it depends on a complex interaction between the environment, the agent, and the host. The analysis of cellular components of M. tuberculosis shows important host-pathogen interactions, metabolic pathways, virulence mechanisms, and mechanisms of adaptation to the environment. However, the M. tuberculosis proteome still remains largely uncharacterized in terms of virulence and pathogenesis. Here, we summarize some of the major proteomic studies performed to scrutinize all the mycobacterial components.

• Journal of Microbiology and Biotechnology
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• v.29 no.2
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• pp.292-296
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• 2019

Soils amended for long-term with high levels of compost demonstrated greater abundance of bacterial members of the phylum Bacteroidetes whereas a decreasing trend in the relative abundance of phylum Acidobacteria was noted with increasing levels of compost. Metabolic profiles predicted by PICRUSt demonstrated differences in functional responses of the bacterial community according to the treatments. Soils amended with lower compost levels were characterized by abundance of genes encoding enzymes contributing to membrane transport and cell growth whereas genes encoding enzymes related to protein folding and transcription were enriched in soils amended with high levels of compost. Thus, the results of the current study provide extensive evidence of the influence of different compost levels on bacterial diversity and community structure in paddy soils.

• Journal of Korean Medicine for Obesity Research
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• v.22 no.1
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• pp.77-85
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• 2022

While the Coronavirus disease 2019 (COVID-19) pandemic is gradually turning into an endemic disease, concerns about post COVID-19 conditions (Long COVID) are emerging. Obesity is a major risk factor for severe complications of COVID-19, and COVID-19 has a wide range of effects on obesity and metabolic function. This paper aims to examine the interaction between COVID-19 and obesity, the effects and mechanisms of long COVID on obesity, and the role of Korean medicine on long COVID-related obesity. Obesity may worsen with cardiometabolic damage and psychosocial insecurity during COVID-19 and long COVID-induced neuroinflammation, systemic inflammation, mitochondrial dysfunction, and hypoxia also may aggravate obesity. Korean Medicine treatments, which have been widely used to treat obesity, have the potential to improve obesity in the era of long COVID by intervening in these mechanisms.

• Genomics & Informatics
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• v.6 no.4
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• pp.210-222
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• 2008

Due to the polygenic nature of cancer, it is believed that breast cancer is caused by the perturbation of multiple genes and their complex interactions, which contribute to the wide aspects of disease phenotypes. A systems biology approach for the identification of subnetworks of interconnected genes as functional modules is required to understand the complex nature of diseases such as breast cancer. In this study, we apply a 3-step strategy for the interpretation of microarray data, focusing on identifying significantly perturbed metabolic pathways rather than analyzing a large amount of overexpressed and underexpressed individual genes. The selected pathways are considered to be dysregulated functional modules that putatively contribute to the progression of disease. The subnetwork of protein-protein interactions for these dysregulated pathways are constructed for further detailed analysis. We evaluated the method by analyzing microarray datasets of breast cancer tissues; i.e., normal and invasive breast cancer tissues. Using the strategy of microarray analysis, we selected several significantly perturbed pathways that are implicated in the regulation of progression of breast cancers, including the extracellular matrix-receptor interaction pathway and the focal adhesion pathway. Moreover, these selected pathways include several known breast cancer-related genes. It is concluded from this study that the present strategy is capable of selecting interesting perturbed pathways that putatively play a role in the progression of breast cancer and provides an improved interpretability of networks of protein-protein interactions.