• Genomics & Informatics
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• v.2 no.4
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• pp.191-194
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• 2004

Exponentially increasing biopathway data in recent years provide us with means to elucidate the large-scale modular organization of the cell. Given the existing information on metabolic and regulatory networks, inferring biopathway information through scientific reasoning or data mining of large scale array data or proteomics data get great attention. Naturally, there is a need for a user-friendly system allowing the user to combine large and diverse pathway data sets from different resources. We built a data warehouse - BIOWAY - for analyzing and visualizing biological pathways, by integrating and customizing resources. We have collected many different types of data in regards to pathway information, including metabolic pathway data from KEGG/LIGAND, signaling pathway data from BIND, and protein information data from SWISS-PROT. In addition to providing general data retrieval mechanism, a successful user interface should provide convenient visualization mechanism since biological pathway data is difficult to conceptualize without graphical representations. Still, the visual interface in the previous systems, at best, uses static images only for the specific categorized pathways. Thus, it is difficult to cope with more complex pathways. In the BIOWAY system, all the pathway data can be displayed in computer generated graphical networks, rather than manually drawn image data. Furthermore, it is designed in such a way that all the pathway maps can be expanded or shrinked, by introducing the concept of super node. A subtle graphic layout algorithm has been applied to best display the pathway data.

• BMB Reports
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• v.37 no.4
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• pp.402-407
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• 2004

A human gene T-complex protein 10 like (TCP10L) was cloned in our lab. A previous study showed that it expressed specifically in the liver and testis. A transcription experiment revealed that TCP10L was a transcription factor with transcription inhibition activity. In this study, the human MAD4 was identified to interact with TCP10L by a yeast two-hybrid screen. This finding was confirmed by immunoprecipitation and subcellular localization experiments. As MAD4 is a member of the MAD family, which antagonizes the functions of MYC and promotes cell differentiation, the biological function of the interaction between TCP10L and MAD4 may be to maintain the differentiation state in liver cells. Also, we propose that the up-regulation of Myc is caused by the down-regulation of TCP10L in human hepatocarcinomas.

• BMB Reports
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• v.51 no.1
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• pp.14-20
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• 2018

Biomedical research involving nanoparticles has produced useful products with medical applications. However, the potential toxicity of nanoparticles in biofluids, cells, tissues, and organisms is a major challenge. The '-omics' analyses provide molecular profiles of multifactorial biological systems instead of focusing on a single molecule. The 'omics' approaches are necessary to evaluate nanotoxicity because classical methods for the detection of nanotoxicity have limited ability in detecting miniscule variations within a cell and do not accurately reflect the actual levels of nanotoxicity. In addition, the 'omics' approaches allow analyses of in-depth changes and compensate for the differences associated with high-throughput technologies between actual nanotoxicity and results from traditional cytotoxic evaluations. However, compared with a single omics approach, integrated omics provides precise and sensitive information by integrating complex biological conditions. Thus, these technologies contribute to extended safety evaluations of nanotoxicity and allow the accurate diagnoses of diseases far earlier than was once possible in the nanotechnology era. Here, we review a novel approach for evaluating nanotoxicity by integrating metabolomics with metabolomic profiling and transcriptomics, which is termed "metabotranscriptomics."

• The Korean Journal of Zoology
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• v.38 no.4
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• pp.570-579
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• 1995

Ultrastructural and histochemical changes of mucous cells In the freshwater and seawater-adapted guppy (Poecflia reticulatus) gills were observed by the light, scanning-and transmisslon~lectron microscopes. The mucous cells were usually located in the epithelium of primary lameilne projected from the gill arch. The rough endoplasmic retIculum and Golgi complex were hIghly developed In immature mucous cells. The mature mucous cells were nearly filled with the mucous granules. In the freshwater guppy, the histochemical properties of the mucous cells were a mixture of the neutral mucin, sialomucin and sulfomucin. When guppy was adapted to the seawater, the content of acid glycoproteins (slalomucln and sulfomucin) was decreased. In addition, the number of mucous cells in the seawater-adapted group was less than a third of those in the freshwater one. These results suggest that the seawater-adapted guppy would react to the changed osmotic stress of the seawater. And also, the environmental change by the increased salt concentraion might lead to reduce the chance of infections.

• The Korean Journal of Zoology
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• v.16 no.1
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• pp.43-53
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• 1973

The flight muscles in Pieris rapae have been examined to study ultrastructural changes in mitochondria with aging. All the mitochondira of flight muscle from the butterfly are recognized as type A which has the simple folded cristae and light matrix, and type B which possesses the complex multicristae and dense matrix. In just newly emerged butterflies both A and B type mitochondria are almost equally present. About ten days after emergence the type A mitochondria rapidly decrease, compared with the type B. In ten-day-old butterflies the type B mitochondria vary in ultrastructure with age. Ultrastructural changes of these aged mitochondria are supposed to occur, in part, by reorganization of inner membranes into myelin-like structures which represent the phase of degeneration of the B type with age. Age-dependent increase in size and number of concentric rings in myelin-like whorl are also found. Glycogen particles penetrated from the cytoplasmic matrix of the muscle cell into the mitochondrial matrix to be in the center of their concentric rings.

• Bulletin of the Korean Chemical Society
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• v.30 no.4
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• pp.897-901
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• 2009

Heme oxygenase-1 (HO-1) is an anti-inflammatory and anti-apoptotic protein and has been applied to various gene therapy researches. However, constitutive expression of HO-1 may induce deleterious side effects. In this research, hypoxia inducible HO-1 expression plasmid, pEpo-SV-HO-1, was constructed with the erythropoietin (epo) enhancer and simian virus 40 (SV40) promoter to avoid these unwanted side effects. Dexamethasone conjugated polyethylenimine (PEI-Dexa) was used as a gene carrier. It was previously reported that dexamethasone protected cardiomyocytes from apoptosis under hypoxia. In this research, PEI-Dexa reduced the caspase-3 level in hypoxic H9C2 cardiomyocytes as a derivative of dexamethasone, suggesting that PEI-Dexa is an anti-apoptotic reagent as well as a gene carrier. pEpo-SV-HO-1 was transfected to H9C2 cardiomyocytes using PEI-Dexa and the cells were incubated under normoxia or hypoxia. HO-1 expression was induced in the pEpo-SV-HO-1 transfected cells under hypoxia. In addition, cell viability under hypoxia was higher in the pEpo-SV-HO-1 transfected cells than the pEpo-SV-Luc transfected cells. Also, caspase-3 level was reduced in the pEpo-SV-HO-1 transfected cells under hypoxia. In addition to the anti-apoptotic effect of PEI-Dexa, hypoxia inducible HO-1 expression by pEpo-SVHO- 1 may be helpful to protect cardiomyocytes under hypoxia. Therefore, pEpo-SV-HO-1/PEI-Dexa complex may be useful for ischemic heart disease gene therapy.

• Clinical and Experimental Reproductive Medicine
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• v.38 no.2
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• pp.68-74
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• 2011

Objective: Previously, we found that oocyte specific homeobox (Obox) 4 plays significant role in completion of meiosis specifically at meiosis I-meiosis II (MI-MII) transition. The purpose of this study was to determine the mechanism of action of $Obox4$ in oocyte maturation by evaluating downstream signal networking. Methods: The $Obox4$ dsRNA was prepared by $in$ $vitro$ transcription and microinjected into the cytoplasm of germinal vesicle oocytes followed by $in$ $vitro$ maturation in the presence or absence of 0.2 mM 3-isobutyl-1-metyl-xanthine. Total RNA was extracted from 200 oocytes of each group using a PicoPure RNA isolation kit then amplified two-rounds. The probe hybridization and data analysis were used by Affymetrix Gene-Chip$^{(R)}$ Mouse Genome 430 2.0 array and GenPlex 3.0 (ISTECH, Korea) software, respectively. Results: Total 424 genes were up (n=80) and down (n=344) regulated after $Obox4$ RNA interference (RNAi). Genes mainly related to metabolic pathways and mitogen-activated protein kinase (MAPK) signaling pathway was changed. Among the protein kinase C (PKC) isoforms, PKC-alpha, beta, gamma were down-regulated and especially the MAPK signaling pathway PKC-gamma was dramatically decreased by $Obox4$ RNAi. In the cell cycle pathway, we evaluated the expression of genes involved in regulation of chromosome separation, and found that these genes were down-regulated. It may cause the aberrant chromosome segregation during MI-MII transition. Conclusion: From the results of this study, it is concluded that $Obox4$ is important upstream regulator of the PKC and anaphase-promoting complex action for maintaining intact germinal vesicle.

• Archives of Pharmacal Research
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• v.21 no.4
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• pp.423-428
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• 1998

The ligand binding signals to a wide variety of seven transmembrane cell surface receptors are transduced into intracellular signals through heterotrimeric G-proteins. Recently, there have been reports which show diverse coupling patterns of ligand-activated receptors to the members of Gq family $\alpha$ subunits. In order to shed some light on these complex signal processing networks, interactions between G$\alpha$q family of G protein and neurokinin-2 receptor as well as muscarinic M$_{1}$ receptor, which are considered to be new thearpeutic targets in asthma, were studied. Using washed membranes from Cos-7 cells co-transfected with different G.alpha.q and receptor cDNAs, the receptors were stimulated with various concentrations of carbachol and neurokinin A and the agonist-dependent release of [$^3H$]inositol phosphates through phospholipase C beta-1 activation was measured. Differential coupling of Gaq family of G-protein to muscarinic M$_{1}$ receptor and neurokinin-2 receptor was observed. The neurokinin-2 receptor shows a ligand-mediated response in membranes co-transfected with G$\alpha$q, G$\alpha$11 and G$\alpha$14 but not G$\alpha$16 and the ability of the muscarinic $M_1$ receptor to activate phospholipase C through G$\alpha$/11 but not G$\alpha$14 and G$\alpha$16 was demonstrated. Clearly G$\alpha$/11 can couple $\M_1$ and neurokinin-2 receptor to activate phospholipase C. But, there are differences in the relative coupling of the G$\alpha$14 and G$\alpha$16 subunits to these receptors.

• Journal of Life Science
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• v.16 no.4
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• pp.704-709
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• 2006

The present study intends to characterize the DNA damage-inducible responses in Caenorhabditis elegans. To study UV-inducible responses in C. elegans, two UV-inducible cDNA clones were isolated from C. elegans by using subtration hybridization method. To investigate the expression of isolated genes, UV100 and UV150, the cellular levels of the transcript were determined by Northern blot analysis after UV-irradiation. The transcripts of isolated gene increased rapidly and reached maximum accumulation after UV-irradiation. Compared to the message levels of control, the levels of maximal increase were approximately 2 folds to UV-irradiation. These results implied that the effects of damaging agents are complex and different regulatory pathways exist for the induction of these genes. To study the function of UV100 and UV150 gene in response to UV irradiation, we carried out a RNAi experiment and investigated the UV sensivity. This result indicated that UV100 gene involved in stage-specific repair pathway or regulated by development.

• Molecules and Cells
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• v.38 no.2
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• pp.105-111
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• 2015

The beta2-adrenergic receptor (${\beta}2AR$) belongs to the G protein coupled receptor (GPCR) family, which is the largest family of cell surface receptors in humans. Extra attention has been focused on the human GPCRs because they have been studied as important protein targets for pharmaceutical drug development. In fact, approximately 40% of marketed drugs directly work on GPCRs. GPCRs respond to various extracellular stimuli, such as sensory signals, neurotransmitters, chemokines, and hormones, to induce structural changes at the cytoplasmic surface, activating downstream signaling pathways, primarily through interactions with heterotrimeric G proteins or through G-protein independent pathways, such as arrestin. Most GPCRs, except for rhodhopsin, which contains covalently linked 11 cis-retinal, bind to diffusible ligands, having various conformational states between inactive and active structures. The first human GPCR structure was determined using an inverse agonist bound ${\beta}2AR$ in 2007 and since then, more than 20 distinct GPCR structures have been solved. However, most GPCR structures were solved as inactive forms, and an agonist bound fully active structure is still hard to obtain. In a structural point of view, ${\beta}2AR$ is relatively well studied since its fully active structure as a complex with G protein as well as several inactive structures are available. The structural comparison of inactive and active states gives an important clue in understanding the activation mechanism of ${\beta}2AR$. In this review, structural features of inactive and active states of ${\beta}2AR$, the interaction of ${\beta}2AR$ with heterotrimeric G protein, and the comparison with ${\beta}1AR$ will be discussed.