• The Plant Pathology Journal
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• 제30권4호
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• pp.367-374
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• 2014

Genomes contain a large number of unique genes which have not been found in other species. Although the origin of such "orphan" genes remains unclear, they are thought to be involved in species-specific adaptive processes. Here, we analyzed seven orphan genes (MoSPC1 to MoSPC7) prioritized based on in planta expressed sequence tag data in the rice blast fungus, Magnaporthe oryzae. Expression analysis using qRT-PCR confirmed the expression of four genes (MoSPC1, MoSPC2, MoSPC3 and MoSPC7) during plant infection. However, individual deletion mutants of these four genes did not differ from the wild-type strain for all phenotypes examined, including pathogenicity. The length, GC contents, codon adaptation index and expression during mycelial growth of the four genes suggest that these genes formed during the evolutionary history of M. oryzae. Synteny analyses using closely related fungal species corroborated the notion that these genes evolved de novo in the M. oryzae genome. In this report, we discuss our inability to detect phenotypic changes in the four deletion mutants. Based on these results, the four orphan genes may be products of de novo gene birth processes, and their adaptive potential is in the course of being tested for retention or extinction through natural selection.

• Molecules and Cells
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• 제40권9호
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• pp.621-631
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• 2017

Vaccinia-related kinase 1 (VRK1) and VRK3 are members of the VRK family of serine/threonine kinases and are principally localized in the nucleus. Despite the crucial roles of VRK1/VRK3 in physiology and disease, the molecular and functional interactions of VRK1/VRK3 are poorly understood. Here, we identified over 200 unreported VRK1/VRK3-interacting candidate proteins by affinity purification and LC-MS/MS. The networks of VRK1 and VRK3 interactomes were found to be associated with important biological processes such as the cell cycle, DNA repair, chromatin assembly, and RNA processing. Interactions of interacting proteins with VRK1/VRK3 were confirmed by biochemical assays. We also found that phosphorylations of XRCC5 were regulated by both VRK1/VRK3, and that of CCNB1 was regulated by VRK3. In liver cancer cells and tissues, VRK1/VRK3 were highly upregulated and its depletion affected cell cycle progression in the different phases. VRK3 seemed to affect S phase progression and G2 or M phase entry and exit, whereas VRK1 affects G1/S transition in the liver cancer, which could be explained by different interacting candidate proteins. Thus, this study not only provides a resource for investigating the unidentified functions of VRK1/VRK3, but also an insight into the regulatory roles of VRK1/VRK3 in biological processes.

• 시스템엔지니어링학술지
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• 제9권1호
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• pp.47-53
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• 2013

The object of this study is to define systematically for outputs of Verification Process among the system life cycle process based on ISO/IEC 15288 for power supply system, which is one of the importance sub-systems to configure the LRT system. Furthermore, to prevent various problem in advance that can occur in the Transition LRT's power supply to be completed Integration. For this purpose, traceability of verification requirement and outputs. should be managed to use verification for system requirement and data processing tool. by system engineering techniques of system life cycle process based on ISO/IEC 15288 to LRT system.

• 한국철도학회:학술대회논문집
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• 한국철도학회 2006년도 추계학술대회 논문집
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• pp.1253-1258
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• 2006

As a global effort to conservate the environment, life cycle assessment(LCA) which considers the environmental impact through the life cycle of a product, from acquiring of resources to scrapping, has been actively applied. The LCA is a tool to calculate quantitatively the environmental impacts caused by products or services through their life cycles. Eco-efficiency need that express value of environmental impact provision EMU and develops in two forms according to use target of Eco-efficiency as a tool that environmental impact of EMU. It is a strategic instrument which assists stakeholders to understand which products, processes or services to target with future investments and which are not by comparing economic and ecological values. The results stand for aggregated information on economical value and environmental impact. Also, In this method, it is important to derive EPI(Environmental Performance Index) and SPI(Service Performance Index) from the sources available. The following is used as one of Eco-efficiency tools to achieve the target performance of processes, products and services for designer or projector. According to the eco-efficiency methodology for EMU developed in this study, the user definition and the DB design were carried out as a basic design of eco-efficiency S/W.

• Molecules and Cells
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• 제42권8호
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• pp.579-588
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• 2019

Gene set enrichment analysis (GSEA) is a popular tool to identify underlying biological processes in clinical samples using their gene expression phenotypes. GSEA measures the enrichment of annotated gene sets that represent biological processes for differentially expressed genes (DEGs) in clinical samples. GSEA may be suboptimal for functional gene sets; however, because DEGs from the expression dataset may not be functional genes per se but dysregulated genes perturbed by bona fide functional genes. To overcome this shortcoming, we developed network-based GSEA (NGSEA), which measures the enrichment score of functional gene sets using the expression difference of not only individual genes but also their neighbors in the functional network. We found that NGSEA outperformed GSEA in identifying pathway gene sets for matched gene expression phenotypes. We also observed that NGSEA substantially improved the ability to retrieve known anti-cancer drugs from patient-derived gene expression data using drug-target gene sets compared with another method, Connectivity Map. We also repurposed FDA-approved drugs using NGSEA and experimentally validated budesonide as a chemical with anti-cancer effects for colorectal cancer. We, therefore, expect that NGSEA will facilitate both pathway interpretation of gene expression phenotypes and anti-cancer drug repositioning. NGSEA is freely available at www.inetbio.org/ngsea.

• Biomolecules & Therapeutics
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• 제29권4호
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• pp.373-383
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• 2021

Atherosclerosis is the deposition of plaque in the main arteries. It is an inflammatory condition involving the accumulation of macrophages and various lipids (low-density lipoprotein [LDL] cholesterol, ceramide, S1P). Moreover, endothelial cells, macrophages, leukocytes, and smooth muscle cells are the major players in the atherogenic process. Sphingolipids are now emerging as important regulators in various pathophysiological processes, including the atherogenic process. Various sphingolipids exist, such as the ceramides, ceramide-1-phosphate, sphingosine, sphinganine, sphingosine-1-phosphate (S1P), sphingomyelin, and hundreds of glycosphingolipids. Among these, ceramides, glycosphingolipids, and S1P play important roles in the atherogenic processes. The atherosclerotic plaque consists of higher amounts of ceramide, glycosphingolipids, and sphingomyelin. The inhibition of the de novo ceramide biosynthesis reduces the development of atherosclerosis. S1P regulates atherogenesis via binding to the S1P receptor (S1PR). Among the five S1PRs (S1PR1-5), S1PR1 and S1PR3 mainly exert anti-atherosclerotic properties. This review mainly focuses on the effects of ceramide and S1P via the S1PR in the development of atherosclerosis. Moreover, it discusses the recent findings and potential therapeutic implications in atherosclerosis.

• Molecules and Cells
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• 제44권12호
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• pp.861-878
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• 2021

The human genome contains many retroviral elements called human endogenous retroviruses (HERVs), resulting from the integration of retroviruses throughout evolution. HERVs once were considered inactive junk because they are not replication-competent, primarily localized in the heterochromatin, and silenced by methylation. But HERVs are now clearly shown to actively regulate gene expression in various physiological and pathological conditions such as developmental processes, immune regulation, cancers, autoimmune diseases, and neurological disorders. Recent studies report that HERVs are activated in patients suffering from coronavirus disease 2019 (COVID-19), the current pandemic caused by SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) infection. In this review, we describe internal and external factors that influence HERV activities. We also present evidence showing the gene regulatory activity of HERV LTRs (long terminal repeats) in model organisms such as mice, rats, zebrafish, and invertebrate models of worms and flies. Finally, we discuss several molecular and cellular pathways involving various transcription factors and receptors, through which HERVs affect downstream cellular and physiological events such as epigenetic modifications, calcium influx, protein phosphorylation, and cytokine release. Understanding how HERVs participate in various physiological and pathological processes will help develop a strategy to generate effective therapeutic approaches targeting HERVs.

• 한국약용작물학회지
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• 제20권1호
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• pp.27-35
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• 2012

This study was conducted to investigate changes in composition of ginsenosides and color of processed ginsengs prepared by different steaming-drying times. Processed ginsengs were prepared from white ginseng with skin by 9-time repeated steaming at $96^{\circ}C$ for 3 hours and followed by hot air-drying at $50^{\circ}C$ for 24 hours. As the times of steaming processes increased, lightness (L value) decreased and redness (a value) increased in color of ginseng powders. Crude saponin contents and ginsenosides compositions in processed ginsengs prepared by different steaming-drying times were investigated using the HPLC method, respecively. Crude saponin contents according to increasing steaming-drying times decreased in some degree. In the case of major ginsenosides, the contents of $Rb_1$, $Rb_2$, Rc, Rd, Rf, Re, $RG_1$, Re were decreased with increase in steamimg times, but those of $Rh_1$, $Rg_3$, $Rk_1$ were increased after especially 3 times of steaming processes. Interestingly, in black ginseng were prepared by 9 times steaming processes, the content of ginsenoside $Rg_3$ was 8.20 mg/g, approximately 18 times higher than that (0.46 mg/g) in red ginseng. In addition, the ratio of the protopanaxadiol group and protopanaxatiol group (PD/PT) were increased from 1.9 to 8.4 due to increasing times of steamming process.

• 통합자연과학논문집
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• 제4권4호
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• pp.255-265
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• 2011

Marine ecosystems are often characterized by a high biological diversity, and it corresponds to a high chemical diversity. Up to present, more than 20,000 new bioactive substances have been isolated from marine organisms, where considerable numbers of these naturally occurring derivatives are developed as potential candidates for pharmaceutical application. In this process, screening of natural products from marine organisms that could potentially inhibit the expression of metalloproteinases has gained a huge popularity. Cancer is considered as one of the deadliest diseases in the medical field. Matrix metalloproteinase (MMPs) can degrade extracellular matrix (ECM) components and play important roles in a variety of biological and pathological processes. Matrix metalloproteinase inhibitors (MMPIs) have been identified as potential therapeutic candidates for metastasis, arthritis, chronic inflammation and wrinkle formation.

• 한국산학기술학회:학술대회논문집
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• 한국산학기술학회 2004년도 춘계학술대회
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• pp.335-338
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• 2004

Life-Cycle Engineering(LCE) is a decision-making methodology that considers environmental and cost needs during the product life-cycle. Environmental conscious design and manufacturing has become more and more important and it has been enforced by governmental regulations and used as trade restriction. LCE involves integrating environmental consideration into new product development including design, material selection, manufacturing processes and distribution of the product to the consumers, plus the end-of-life management such as disassembly, material recovery, remanufacturing of the product after discarding it. In this paper, a state-of-the-art survey of LCE is presented.