• BMB Reports
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• v.48 no.11
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• pp.597-598
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• 2015

Mitochondrial respiratory defect is a key bioenergetics feature of hepatocellular carcinoma (HCC) cells. However, their involvement and roles in HCC development and progression remain unclear. Recently, we identified 10 common mitochondrial defect (CMD) signature genes that may be induced by retrograde signaling-mediated transcriptional reprogramming in response to HCC mitochondrial defects. HCC patients with enriched expression of these genes had poor prognostic outcomes, such as shorter periods of overall survival and recurrence-free survival. Nuclear protein 1 (NUPR1), a key transcription regulator, was up-regulated by Ca⁺⁺-mediated retrograde signaling. NUPR1-centric network analysis and a biochemical promoter-binding assay demonstrated that granulin (GRN) is a key downstream effector of NUPR1 for the regulation of HCC cell invasiveness; association analysis of the NUPR1-GRN pathway supported this conclusion. Mitochondrial respiratory defects and retrograde signaling thus play pivotal roles in HCC progression, highlighting the potential of the NUPR1-GRN axis as a novel diagnostic marker and therapeutic target for HCC.

• BMB Reports
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• v.49 no.7
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• pp.370-375
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• 2016

Ras oncoproteins are small molecular weight GTPases known for their involvement in oncogenesis, which operate in a complex signaling network with multiple effectors. Approximately 25% of human tumors possess mutations in a member of this family. The Raf1/MEK/Erk1/2 pathway is one of the most intensively studied signaling mechanisms. Different levels of regulation account for the inactivation of MAP kinases by MAPK phosphatases in a cell type- and stimuli-dependent manner. In the present study, using three inducible Ras-expressing NIH/3T3 cell lines, we demonstrated that MKP3 upregulation requires the activation of the Erk1/2 pathway, which correlates with the shutdown of this pathway. We also demonstrated, by applying pharmacological inhibitors and effector mutants of Ras, that induction of MKP3 at the protein level is positively regulated by the oncogenic Ras/Raf/MEK/Erk1/2 signaling pathway.

• Journal of Korean Institute of Industrial Engineers
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• v.31 no.3
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• pp.257-264
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• 2005

This paper suggests a heuristic algorithm for the clustering problem. Clustering involves grouping similar objects into a cluster. Clustering is used in a wide variety of fields including data mining, marketing, and biology. Until now there are a lot of approaches using Self-Organizing Feature Maps(SOFMs). But they have problems with a small output-layer nodes and initial weight. For example, one of them is a one-dimension map of k output-layer nodes, if they want to make k clusters. This approach has problems to classify elaboratively. This paper suggests one-dimensional output-layer nodes in SOFMs. The number of output-layer nodes is more than those of clusters intended to find and the order of output-layer nodes is ascending in the sum of the output-layer node's weight. We can find input data in SOFMs output node and classify input data in output nodes using Euclidean distance. We use the well known IRIS data as an experimental data. Unsupervised clustering of IRIS data typically results in 15 - 17 clustering error. However, the proposed algorithm has only six clustering errors.

• IMMUNE NETWORK
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• v.12 no.4
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• pp.148-154
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• 2012

Previously, we have reported that high mobility group box 1 (HMGB1), a proinflammatory mediator in sepsis, is released via the IFN-${\beta}$-mediated JAK/STAT pathway. However, detailed mechanisms are still unclear. In this study, we dissected upstream signaling pathways of HMGB1 release using various molecular biology methods. Here, we found that calcium/calmodulin-dependent protein kinase (CaM kinase, CaMK) is involved in HMGB1 release by regulating IFN-${\beta}$ production. CaMK inhibitor, STO609, treatment inhibits LPS-induced IFN-${\beta}$ production, which is correlated with the phosphorylation of interferon regulatory factor 3 (IRF3). Additionally, we show that CaMK-I plays a major role in IFN-${\beta}$ production although other CaMK members also seem to contribute to this event. Furthermore, the CaMK inhibitor treatment reduced IFN-${\beta}$ production in a murine endotoxemia. Our results suggest CaMKs contribute to HMGB1 release by enhancing IFN-${\beta}$ production in sepsis.

• BMB Reports
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• v.46 no.12
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• pp.600-605
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• 2013

Interplay between calcium ions ($Ca^{2+}$) and reactive oxygen species (ROS) delicately controls diverse pathophysiological functions of vascular smooth muscle cells (VSMCs). However, details of the $Ca^{2+}$ and ROS signaling network have been hindered by the absence of a method for dual measurement of $Ca^{2+}$ and ROS. Here, a real-time monitoring system for $Ca^{2+}$ and ROS was established using a genetically encoded hydrogen peroxide indicator, HyPer, and a ratiometric $Ca^{2+}$ indicator, fura-2. For the simultaneous detection of fura-2 and HyPer signals, 540 nm emission filter and 500 nm~ dichroic beamsplitter were combined with conventional exciters. The wide excitation spectrum of HyPer resulted in marginal cross-contamination with fura-2 signal. However, physiological $Ca^{2+}$ transient and hydrogen peroxide were practically measurable in HyPer-expressing, fura-2-loaded VSMCs. Indeed, distinct $Ca^{2+}$ and ROS signals could be successfully detected in serotonin-stimulated VSMCs. The system established in this study is applicable to studies of crosstalk between $Ca^{2+}$ and ROS.

• Journal of KIISE:Software and Applications
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• v.31 no.10
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• pp.1266-1275
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• 2004

Bioinformatics is concerned with the creation and development of advanced information and computational technologies for problems in biology. It is divided into genomics, proteomics and metabolimics. In metabolimics, an organism is represented by metabolic pathway, i.e., well-displayed graph, and so the graph drawing tool to draw pathway well is necessary to understand it comprehensively. In this paper, we design an improved drawing algorithm. It enhances the readability by making use of the bipartite graph. Also it is possible to draw large graph properly by considering the facts that metabolic pathway graph is scale-free network and is composed of circular components, hierarchic components and linear components.

• Journal of Dairy Science and Biotechnology
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• v.30 no.1
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• pp.37-44
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• 2012

Milk-derived bioactive peptides have been found to exhibit various physiological activities such as angiotensin-converting enzyme (ACE) inhibitory, antibacterial, and antioxidative effects. Bioactive peptides can be used in the formulation of functional foods, nutraceuticals, and natural drugs because of their beneficial effects. However, the degree of variability in the composition, functionality, and sensory properties of such peptides has greatly limited their use in the food industry. In this review, we discuss the main peptides obtained from milk proteins and summarize findings from previous studies on the production and biological activities of these peptides. In addition, we compare the methods used to separate and identify the structure of the bioactive peptides and highlight current investigations into engineering and implementation of technologies that would allow more efficient isolation of bioactive peptides for functional food production. To improve human health, further molecular biology studies will also be required to elucidate the complex network of interactions between food microorganisms and the digestive system.

• Macromolecular Research
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• v.17 no.6
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• pp.424-429
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• 2009

In this study, we demonstrate that the biological unnatural amino acid incorporation method can be utilized in vivo to synthesize an alkyne-terminated telechelic protein, Synthesis of terminally-functionalized polymers such as telechelic polymers is recognized to be important, since they can be employed usefully in many areas of biology and material science, such as drug delivery, colloidal dispersion, surface modification, and formation of polymer network. The introduction of alkyne groups into polymeric material is particularly interesting since the alkyne group can be a linker to combine other materials using click chemistry. To synthesize the telechelic recombinant protein, we attempted to incorporate the L-homopropargylglycine into the recombinant GroES fragment by expressing the recombinant gene encoding Met at the codons for both N- and C-terminals of the protein in the Met auxotrophic E. coli via Hpg supplementation. The Hpg incorporation rate was investigated and the incorporation was confirmed by MALDI-TOF analysis of the telcchelic recombinant protein.

• Molecules and Cells
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• v.43 no.7
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• pp.600-606
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• 2020

Numerous physiological processes in nature have multiple oscillations within 24 h, that is, ultradian rhythms. Compared to the circadian rhythm, which has a period of approximately one day, these short oscillations range from seconds to hours, and the mechanisms underlying ultradian rhythms remain largely unknown. This review aims to explore and emphasize the implications of ultradian rhythms and their underlying regulations. Reproduction and developmental processes show ultradian rhythms, and these physiological systems can be regulated by short biological rhythms. Specifically, we recently uncovered synchronized calcium oscillations in the organotypic culture of hypothalamic arcuate nucleus (ARN) kisspeptin neurons that regulate reproduction. Synchronized calcium oscillations were dependent on voltage-gated ion channel-mediated action potentials and were repressed by chemogenetic inhibition, suggesting that the network within the ARN and between the kisspeptin population mediates the oscillation. This minireview describes that ultradian rhythms are a general theme that underlies biological features, with special reference to calcium oscillations in the hypothalamic ARN from a developmental perspective. We expect that more attention to these oscillations might provide insight into physiological or developmental mechanisms, since many oscillatory features in nature still remain to be explored.

• IMMUNE NETWORK
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• v.13 no.6
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• pp.249-256
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• 2013

How Th2 immunity develops in vivo remains obscure. Basophils have been considered key innate cells producing IL-4, a cytokine essential for Th2 immunity. Increasing evidence suggests that basophils are dispensable for the initiation of Th2 immunity. In this study, we revisited the role of basophils in Th2 immune responses induced by various types of adjuvants. Mice deficient in IL-3 or IL-3 receptor, in which basophil lymph node recruitment is completely abolished, fully developed wild type level Th2 CD4 T cell responses in response to parasite antigen or papain immunization. Similar finding was also observed in mice where basophils are inducibly ablated. Interestingly, IL-4-derived from non-T cells appeared to be critical for the generation of IL-4-producing CD4 T cells. Other Th2 promoting factors including IL-25 and thymic stromal lymphopoietin (TSLP) were dispensable. Therefore, our results suggest that IL-3- and basophil-independent in vivo Th2 immunity develops with the help of non-T cell-derived IL-4, offering an additional mechanism by which Th2 type immune responses arise in vivo.