• Journal of Life Science
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• v.29 no.4
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• pp.436-441
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• 2019

Nelumbo nucifera, also known as sacred lotus, has mainly been used as a food throughout the Asian countries. In the present study, we prepared ethanol extracts from leaf (NL), seed (NS), and seedpod (NSP) of Nelumbo nucifera and investigated their anti-inflammatory activities in mouse macrophage RAW 264.7 cells. To evaluate the anti-inflammatory activities of NL, NS, and NSP, nitric oxide (NO) production was measured in LPS-stimulated RAW 264.7 cells. NL, NS, and NSP significantly reduced NO production in a dose-dependent manner without affecting cell viabilities. NL, NS, and NSP dramatically decreased the protein expression of pro-inflammatory genes such as iNOS and COX-2. NL, NS, and NSP also suppressed phosphorylation of MAPKs and the nuclear translocation of $NF-{\kappa}B$ p65 indicating they have their anti-inflammatory activities via regulating mitogen-activated protein kinases (MAPKs) and nuclear factor kappa B ($NF-{\kappa}B$) pathways. In addition, we analyzed the production of reactive oxygen species (ROS) by the treatment of NL, NS, and NSP. All extracts reduced ROS production in a dose-dependent manner. And also, they increased heme oxygenase-1 (HO-1) protein expression and the nuclear translocation of nuclear respiratory factor 2 (Nrf2). In conclusion, our results suggest that Nelumbo nucifera has its anti-inflammatory activity via regulating MAPKs, $NF-{\kappa}B$, and Nrf2/HO-1 pathways.

• BMB Reports
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• v.42 no.2
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• pp.65-71
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• 2009

Autophagy, which is a process of self eating, has gained interest in the past decade due to its both beneficial and controversial roles in various biological phenomena. The discovery of autophagy genes (ATG) in yeast has led to focused research designed to elucidate the mechanism and regulation of this process. The role of autophagy in a variety of biological phenomena, including human disease, is still the subject of debate. However, recent findings suggest that autophagy is a highly regulated process with both beneficial and negative effects. Indeed, studies conducted using various model organisms have demonstrated that increased autophagy leads to an extended lifespan. Despite these findings, it is still unknown if all pathways leading to extended lifespan converge at the process of autophagy or not. Here, an overview of modern developments related to the process of autophagy, its regulation and the molecular machinery involved is presented. In addition, this review focuses on one of the beneficial aspects of autophagy, its role in lifespan regulation.

• Journal of Applied Biological Chemistry
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• v.51 no.3
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• pp.83-87
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• 2008

Tension wood, a specialized tissue developed in the upper side of the leaning stem and drooping branches of angiosperm, is an attractive experimental system attractive for exploring the development and the biochemical pathways of the secondary cell wall formation, as well as the control mechanism of the carbon flux into lignin, cellulose, and hemicellulose. However, the mechanism underlying the induction and the development of the tension wood is largely unknown. Recently, several researchers suggested the possible roles of the plant growth hormones including auxin, gibberellin, and ethylene mainly based on the expression pattern of the genes in this specialized tissue. In addition, expressed sequence tag of Poplar and Eucalyptus provide global view of the genetic control underlying the tension wood formation. However, the roles of the majority of the identified genes have not yet been clearly elucidated. The present review summarized current knowledge on the biosynthesis of tension wood to provide a brief synopsis of the molecular mechanism underlying the development of the tension wood.

• Molecules and Cells
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• v.41 no.4
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• pp.257-263
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• 2018

Vertebrate organ development is accompanied by demarcation of tissue compartments, which grow coordinately with their neighbors. Hence, perturbing the coordinative growth of neighboring tissue compartments frequently results in organ malformation. The growth of tissue compartments is regulated by multiple intercellular and intracellular signaling pathways, including the Hippo signaling pathway that limits the growth of various organs. In the optic neuroepithelial continuum, which is partitioned into the retina, retinal pigment epithelium (RPE) and ciliary margin (CM) during eye development, the Hippo signaling activity operates differentially, as it does in many tissues. In this review, we summarize recent studies that have explored the relationship between the Hippo signaling pathway and growth of optic neuroepithelial compartments. We will focus particularly on the roles of a tumor suppressor, neurofibromin 2 (NF2), whose expression is not only dependent on compartment-specific transcription factors, but is also subject to regulation by a Hippo-Yap feedback signaling circuit.

• Biomolecules & Therapeutics
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• v.26 no.4
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• pp.350-357
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• 2018

Glial cells are receiving much attention since they have been recognized as important regulators of many aspects of brain function and disease. Recent evidence has revealed that two different glial cells, astrocytes and microglia, control synapse elimination under normal and pathological conditions via phagocytosis. Astrocytes use the MEGF10 and MERTK phagocytic pathways, and microglia use the classical complement pathway to recognize and eliminate unwanted synapses. Notably, glial phagocytosis also contributes to the clearance of disease-specific protein aggregates, such as ${\beta}$-amyloid, huntingtin, and ${\alpha}$-synuclein. Here we reivew recent findings showing that glial cells are active regulators in brain functions through phagocytosis and that changes in glial phagocytosis contribute to the pathogenesis of various neurodegenerative diseases. A better understanding of the cellular and molecular mechanisms of glial phagocytosis in healthy and diseased brains will greatly improve our current approach in treating these diseases.

• Journal of Applied Biological Chemistry
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• v.50 no.2
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• pp.58-62
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• 2007

Identification of Dual-specificity protein phosphatase (DSP) substrates is essential in revealing physiological roles of DSPs. We isolated VHZ-interacting proteins from extracts of 293T cells overexpressing a VHZ (C95S, D65A) mutant known to be substrate- trapping mutant. Analysis of specific proteins bound to VHZ by 2D gel electrophoresis and mass spectroscopy revealed that these proteins contained Chaperonin containing TCP1, Type II phosphatidylinositol phosphate kinase ${\gamma}$, Intraflagellar transport 80 homolog, and Kinesin superfamily protein 1B. VHZ-interacting proteins showed that VHZ is involved in many important cellular signal pathways such as protein folding, molecular transportation, and tumor suppression.

• Journal of the Korean Magnetic Resonance Society
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• v.17 no.1
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• pp.1-10
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• 2013

Metabolomics is the study which detects the changes of metabolites level. Metabolomics is a terminal view of the biological system. The end products of the metabolism, metabolites, reflect the responses to external environment. Therefore metabolomics gives the additional information about understanding the metabolic pathways. These metabolites can be used as biomarkers that indicate the disease or external stresses such as exposure to toxicant. Many kinds of biological samples are used in metabolomics, for example, cell, tissue, and bio fluids. NMR spectroscopy is one of the tools of metabolomics. NMR data are analyzed by multivariate statistical analysis and target profiling technique. Recently, NMR-based metabolomics is a growing field in various studies such as disease diagnosis, forensic science, and toxicity assessment.

• Genomics & Informatics
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• v.1 no.1
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• pp.7-19
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• 2003

The latest measure of the relative evolutionary age of protein structure families was applied (based on taxonomic diversity) using the protein structural interactome map (PSIMAP). It confirms that, in general, protein domains, which are hubs in this interaction network, are older than protein domains with fewer interaction partners. We apply a hypothesis of 'biological network evolution' to explain the positive correlation between interaction and age. It agrees to the previous suggestions that proteins have acquired an increasing number of interaction partners over time via the stepwise addition of new interactions. This hypothesis is shown to be consistent with the scale-free interaction network topologies proposed by other groups. Closely co-evolved structural interaction and the dynamics of network evolution are used to explain the highly conserved core of protein interaction pathways, which exist across all divisions of life.

• BMB Reports
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• v.51 no.10
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• pp.493-499
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• 2018

Cellular senescence is a state of permanent cell-cycle arrest triggered by different internal and external stimuli. This phenomenon is considered to be both beneficial and detrimental depending on the cell types and biological contexts. During normal embryonic development and after tissue injury, cellular senescence is critical for tissue remodeling. In addition, this process is useful for arresting growth of tumor cells, particularly during early onset of tumorigenesis. However, accumulation of senescent cells decreases tissue regenerative capabilities and induces inflammation, which is responsible for cancer and organismal aging. Therefore cellular senescence has to be tightly regulated, and dysregulation might lead to the aging and human diseases. Among many regulators of cellular senescence, in this review, I will focus on microRNAs, small non-coding RNAs playing critical roles in diverse biological events including cellular senescence.

• Molecules and Cells
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• v.25 no.2
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• pp.279-288
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• 2008

The analysis of microarray data is essential for large amounts of gene expression data. In this review we focus on clustering techniques. The biological rationale for this approach is the fact that many co-expressed genes are co-regulated, and identifying co-expressed genes could aid in functional annotation of novel genes, de novo identification of transcription factor binding sites and elucidation of complex biological pathways. Co-expressed genes are usually identified in microarray experiments by clustering techniques. There are many such methods, and the results obtained even for the same datasets may vary considerably depending on the algorithms and metrics for dissimilarity measures used, as well as on user-selectable parameters such as desired number of clusters and initial values. Therefore, biologists who want to interpret microarray data should be aware of the weakness and strengths of the clustering methods used. In this review, we survey the basic principles of clustering of DNA microarray data from crisp clustering algorithms such as hierarchical clustering, K-means and self-organizing maps, to complex clustering algorithms like fuzzy clustering.