Hak Yong Kim

Chungbuk National University, Tyundyu, North Chungcheong, South Korea

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Publications (17)25.61 Total impact

  • Hyun-Il Shin, Hak Yong Kim, Tae-Ju Cho
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    ABSTRACT: Turnip yellow mosaic virus (TYMV) is a spherical plant virus that has a single 6.3 kb positive strand RNA. The genomic RNA has a tRNA-like structure (TLS) at the 3'-end. The 3'-TLS and hairpins in the 5'-untranslated region supposedly serve as packaging signals; however, recent studies have shown that they do not play a role in TYMV RNA packaging. In this study, we focused on packaging signals by examining a series of deletion mutants of TYMV. Analysis of encapsidated viral RNA after agroinfiltration of the deletion constructs into Nicotiana benthamiana showed that the mutant RNA lacking the protease (Pro)/helicase (Hel) region was not encapsidated by the coat proteins provided in trans, implicating that a packaging signal lies in the Pro/Hel region. Examination of two Pro(-)Hel(-) mutants showed that protein activity from the Pro/Hel domains was dispensable for the packaging of the non-replicating TYMV RNA. In contrast, the mutant TYMV RNA lacking the Pro/Hel region was efficiently encapsidated when the mutant TYMV was co-introduced with a wild-type TYMV, suggesting that packaging mechanisms might differ depending on whether the virus is replicating or not.
    Molecules and Cells 05/2010; 29(5):463-9. · 2.21 Impact Factor
  • Tae Ho Kang, Jae Soo Yoo, Hak Yong Kim
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    ABSTRACT: Biological sequences such as DNA and amino acid sequences typically contain a large number of items. They have contiguous sequences that ordinarily consist of more than hundreds of frequent items. In biological sequences analysis (BSA), a frequent contiguous sequence search is one of the most important operations. Many studies have been done for mining sequential patterns efficiently. In recent years, the MacosVSpan algorithm was proposed based on the idea of the prefixSpan algorithm to significantly reduce its recursive process. However, the algorithm is inefficient for mining frequent contiguous sequences from long biological data sequences. In this paper, we propose an efficient method to mine maximal frequent contiguous sequences in large biological data sequences by constructing the spanning tree with a fixed length. To verify the superiority of the proposed method, we perform experiments in various environments. The experiments show that the proposed method is much more efficient than MacosVSpan in terms of retrieval performance.
    Bioinformatics and Bioengineering, 2007. BIBE 2007. Proceedings of the 7th IEEE International Conference on; 11/2007
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    ABSTRACT: Angiogenin, a potent angiogenic factor, binds to endothelial cells and is endocytosed and rapidly translocated to and concentrated in the nucleolus where it binds to DNA. In this study, we report that angiogenin induces transient phosphorylation of protein kinase B/Akt in cultured human umbilical vein endothelial (HUVE) cells. LY294002 inhibits the angiogenin-induced protein kinase B/Akt activation and also angiogenin-induced cell migration in vitro as well as angiogenesis in chick embryo chorioallantoic membrane in vivo without affecting nuclear translocation of angiogenin in HUVE cells. These results suggest that cross-talk between angiogenin and protein kinase B/Akt signaling pathways is essential for angiogenin-induced angiogenesis in vitro and in vivo, and that angiogenin-induced PKB/Akt activation is independent of nuclear translocation of angiogenin in HUVE cells.
    Biochemical and Biophysical Research Communications 02/2007; 352(2):509-13. · 2.28 Impact Factor
  • Journal- Korean Physical Society 01/2007; 51. · 0.51 Impact Factor
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    ABSTRACT: Recently, several studies have focused on the transcriptional regulation of gene expression in Saccharomyces cerevisiae. In this study, we investigate the regulation of gene expression by 106 transcription factors in S. cerevisiae based on the genome-wide location analysis data of Lee et al. (Science vol. 298, 2002). By computational methods, we analyze the positions of genes regulated by 106 transcription factors on 16 chromosomes. The chromosome-wide distribution of regulated genes by 106 transcription factors is rather uniform over the 16 chromosomes. However, a detailed posi-tional correlation analysis among target genes of the transcription factors shows that nearby genes have more chances to be co-regulated by the transcription factor. As a consequence of positional co-regulation, we have identified the presence of 2-, 3-, 4-, 5-, and 6-gene motif structures, called "operon-like motif structures", in which n-genes are sequentially regulated by the same transcrip-tion factor. To understand the functional role of the operon-like motif structure, we investigate the correlation of gene expression for these motif genes. The analysis shows a high correlation among genes in the motifs compared to random gene pairs. This result indicates that genes in operon-like motif structures are functionally correlated.
    Journal- Korean Physical Society 01/2007; Vol. 50(No. 1):pp. 332-�336. · 0.51 Impact Factor
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    ABSTRACT: Angiogenin is one of the most potent angiogenesis-inducing proteins. Angiostatin is one of the most potent angiogenesis inhibitors, and it contains the first four kringle domains of plasminogen (K1-4). Recombinant human plasminogen kringle 1-3 (rK1-3) was expressed in Escherichia coli and purified to homogeneity. The binding of t-4-aminomethylcyclohexanecarboxylic acid with the purified kringle 1-3 was determined by changes in intrinsic fluorescence. rK1-3 exhibits comparable ligand-binding properties as native human plasminogen kringle 1-3. The purified rK1-3 inhibits neovascularization in the chick embryo chorioallantoic membrane (CAM) assay. Interaction of angiogenin with rK1-3 was examined by immunological binding assay and surface plasmon resonance kinetic analysis, and the equilibrium dissociation constants for the complex, Kd, are 0.89 and 0.18 microM, respectively. rK1-3 inhibits angiogenin-induced angiogenesis in the chick embryo CAM in a concentration-dependent manner. These results indicate that rK1-3 directly binds to angiogenin and thus rK1-3 inhibits the angiogenic activity of angiogenin.
    Biochemical and Biophysical Research Communications 06/2006; 343(3):917-23. · 2.28 Impact Factor
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    ABSTRACT: Endostatin is a tumor-derived angiogenesis inhibitor, and the endogenous 20 kDa carboxyl-terminal fragment of collagen XVIII. In addition to inhibiting angiogenesis,endostatin inhibits tumor growth and the induction of apoptosis in several endothelial cell types. However, the mechanisms that regulate endostatin-induced apoptotic cell death are unclear. Here, we investigated apoptotic cell death and the underlying regulatory mechanisms elicited of endostatin in human umbilical vein endothelial cells (HUVECs). Endostatin was found to induce typical apoptotic features, such as, chromatin condensation and DNA fragmentation in these cells. Thus, as the phosphoinositide 3-OH kinase (PI3K)/protein kinase B (PKB) signaling pathway has been shown to prevent apoptosis in various cell types, we investigated whether this pathway could protect cells against endostatin induced apoptosis. It was found that the inhibition of PI3K/PKB significantly increased endostatin-induced apoptosis, and that endostatininduced cell death is physiologically linked to PKB-mediated cell survival through caspase-8.
    Journal of biochemistry and molecular biology 02/2006; 39(1):97-104. · 2.02 Impact Factor
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    ABSTRACT: Pseudomonas syringae pv. tomato (Pst) causes a bacterial speck disease in tomato and Arabidopsis. In Chinese cabbage, in which host-pathogen interactions are not well understood, Pst does not cause disease but rather elicits a hypersensitive response. Pst induces localized cell death and H2O2 accumulation, a typical hypersensitive response, in infiltrated cabbage leaves. Pre-inoculation with Pst was found to induce resistance to Erwinia carotovora subsp. carotovora, a pathogen that causes soft rot disease in Chinese cabbage. An examination of the expression profiles of 12 previously identified Pst-inducible genes revealed that the majority of these genes were activated by salicylic acid or BTH; however, expressions of the genes encoding PR4 and a class IV chitinase were induced by ethephon, an ethylene-releasing compound, but not by salicylic acid, BTH, or methyl jasmonate. This implies that Pst activates both salicylate-dependent and salicylate-independent defense responses in Chinese cabbage.
    Journal of biochemistry and molecular biology 12/2005; 38(6):748-54. · 2.02 Impact Factor
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    ABSTRACT: Crystalline structures of cellulose (named as Cell 1), NaOH-treated cellulose (Cell 2), and subsequent CO2-treated cellulose (Cell 2-C) were analyzed by wide-angle X-ray diffraction and FTIR spectroscopy. Transformation from cellulose I to cellulose II was observed by X-ray diffraction for Cell 2 treated with 15-20 wt% NaOH. Subsequent treatment with CO2 also transformed the Cell 2-C treated with 5-10 wt% NaOH. Many of the FTIR bands including 2901, 1431, 1282, 1236, 1202, 1165, 1032, and 897 cm(-1) were shifted to higher wave number (by 2-13 cm(-1)). However, the bands at 3352, 1373, and 983 cm(-1) were shifted to lower wave number (by 3-95 cm(-1)). In contrast to the bands at 1337, 1114, and 1058 cm(-1), the absorbances measured at 1263, 993, 897, and 668 cm(-1) were increased. The FTIR spectra of hydrogen-bonded OH stretching vibrations at around 3352 cm(-1) were resolved into three bands for cellulose I and four bands for cellulose II, assuming that all the vibration modes follow Gaussian distribution. The bands of 1 (3518 cm(-1)), 2 (3349 cm(-1)), and 3 (3195 cm(-1)) were related to the sum of valence vibration of an H-bonded OH group and an intramolecular hydrogen bond of 2-OH ...O-6, intramolecular hydrogen bond of 3-OH...O-5 and the intermolecular hydrogen bond of 6-O...HO-3', respectively. Compared with the bands of cellulose I, a new band of 4 (3115 cm(-1)) related to intermolecular hydrogen bond of 2-OH...O-2' and/or intermolecular hydrogen bond of 6-OH...O-2' in cellulose II appeared. The crystallinity index (CI) was obtained by X-ray diffraction [CI(XD)] and FTIR spectroscopy [CI(IR)]. Including absorbance ratios such as A1431,1419/A897,894 and A1263/A1202,1200, the CI(IR) was evaluated by the absorbance ratios using all the characteristic absorbances of cellulose. The CI(XD) was calculated by the method of Jayme and Knolle. In addition, X-ray diffraction curves, with and without amorphous halo correction, were resolved into portions of cellulose I and cellulose II lattice. From the ratio of the peak area, that is, peak area of cellulose I (or cellulose II)/total peak area, CI(XD) were divided into CI(XD-CI) for cellulose I and CI(XD-CII) for cellulose II. The correlation between CI(XD-CI) (or CI(XD-CII)) and CI(IR) was evaluated, and the bands at 2901 (2802), 1373 (1376), 897 (894), 1263, 668 cm(-1) were good for the internal standard (or denominator) of CI(IR), which increased the correlation coefficient. Both fraction of the absorbances showing peak shift were assigned as the alternate components of CI(IR). The crystallite size was decreased to constant value for Cell 2 treated at >or= 15 wt% NaOH. The crystallite size of Cell 2-C (cellulose II) was smaller than that of Cell 2 (cellulose I) treated at 5-10 wt% NaOH. But the crystallite size of Cell 2-C (cellulose II) was larger than that of Cell 2 (cellulose II) treated at 15-20 wt% NaOH.
    Carbohydrate Research 11/2005; 340(15):2376-91. · 2.04 Impact Factor
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    ABSTRACT: Sodium cellulose carbonate (CC-Na) dissolved in 8.5 wt% NaOH/ZnO (100/2–3, w/w) aqueous solution was spun into some acidic coagulant systems. Diameter of regenerated cellulose fibers obtained was in the range of 15–50µm. Serrated or circular cross sectional views were obtained by controlling salt concentration or acidity in the acid/salt/water coagulant systems. Velocity ratio of take-up to spinning was controlled up to 4/1 with increasing spinning velocity from 5 to 40 m/min. Skin structure of was developed at lower acidity or higher concentration of coagulants. Fineness, tenacity and elongation of the regenerated cellulose fibers were in the range of 1.5–27 denier, 1.2–2.2 g/d, and 8–11.3%, respectively. All of CC-Na and cellulose fibers spun from CC-Na exhibited cellulose II crystalline structure. Crystallinity index was increased with increasing take-up speed.
    Fibers and Polymers 01/2005; 6(2):95-102. · 1.11 Impact Factor
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    Hee Young Kang, Hak Yong Kim
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    ABSTRACT: We have constructed protein networks of kinome and cell cycle from MIPS database. The networks show character of scale free network, in which a few highly connected proteins play a central role in most cells. Protein-protein interaction database obtained from a yeast two hybrid screen or a composite data set includes random false positives. To purify the database, we employed cellular localization and DNA expression profile and then reconstructed kinome and cell cycle networks. The kinome and cell cycle networks constructed from the purified database show characters of scale free network and hierarchical network, in which preserves it's scale-free organization and displays inherent modularity of protein clusters. To find functional modules from the network, we propose a new technique that is based on multi-body correlations in kinome or cell cycle network. From the derived modules, we predicted and estimated tentative functions for unannotated proteins with high certainty.
    Computational Systems Bioinformatics Conference, 2004. CSB 2004. Proceedings. 2004 IEEE; 09/2004
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    ABSTRACT: Actinomycin D (act-D) anchors itself into DNA-base pairs by intercalation and thereby inhibits mRNA synthesis. It has been well established that act-D elicits apoptosis in various cell types involving endothelial cells. However, the regulatory mechanisms of actinomycin D-induced apoptotic cell death still remain unclear. Here, we investigated apoptotic cell death and its underlying regulatory mechanisms elicited by actinomycin D in ECV304. Act-D induced typical apoptotic features including chromatin condensation and translocation of phosphatidylserine. Since the phosphoinositide 3-OH kinase (PI3K)/protein kinase B (PKB) signaling pathway has been shown to prevent apoptosis in various cell types, it was of interest to determine if this pathway could protect against apoptosis induced by act-D. Inhibition of PI3K/PKB significantly increased act-D-induced apoptosis. Moreover, act-D-induced cell death was physiologically linked to PKB-mediated cell survival through caspase-8. These results suggest that cross-talk between the PKB and caspase-8 pathways may regulate the balance between cell survival and cell death in ECV304.
    Archives of Biochemistry and Biophysics 06/2004; 425(2):214-20. · 3.37 Impact Factor
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    ABSTRACT: Atactic poly(vinyl alcohols) (a-PVAs) having number-average degrees of polymerization [(Pn)s] of 1700 and 4000 were prepared by the solution polymerization of vinyl acetate, which was followed by the saponification of poly(vinyl acetate) to investigate the effects of molecular weights of a-PVA on the characteristics of electrospun a-PVA nanofabrics. A-PVA nanofabrics were prepared by electrospinning with controlling the process parameters including the electrical field, conductivity, tip-to-collector distance, and solution concentration. Through a series of characterization experiments, we identified that the molecular weight of a-PVA had a marked influence on the structure and properties of nanofabrics produced. That is, the higher the molecular weight of PVA, the superior the physical properties of PVA nanofabric. © 2004 Wiley Periodicals, Inc. J Appl Polym Sci 93: 1638–1646, 2004
    Journal of Applied Polymer Science 05/2004; 93(4):1638 - 1646. · 1.40 Impact Factor
  • Chang No Yoon, Seung Kee Han, Hak Yong Kim
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    ABSTRACT: linear network model with periodic regulator terms for the estimation of the gene regulation network of the cell cycle. Microarray gene expression data for yeast are used for the construction of a gene regulation network for 40 genes in the G2/M or G1 phase. It is shown that the periodic regulator terms faithfully represent the phase information, and the weight matrix elements contain several up- and down-regulation terms among genes in the G2/M and G1 phase.
    Journal- Korean Physical Society 03/2004; 44(3). · 0.51 Impact Factor
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    ABSTRACT: We have developed a subtractive cloning method in which target sequences are effectively enriched by selective adaptor ligation and PCR after hybridization. In this method both tester and driver DNAs are digested with RsaI, ligated with the linker DNA containing a KpnI recognition site, and amplified by PCR. The tester DNA samples are divided into two aliquots, each digested with either RsaI or KpnI. The two DNA samples are then combined and hybridized with an excess of the driver DNA retaining the linker. After hybridization, the DNA mixture is ligated to a new adaptor compatible only with double-stranded tester/tester DNAs. Therefore, only the tester/tester is selectively amplified in subsequent PCR. This also leads to complete elimination of the tester DNA hybridized with driver DNA from the tester DNA population. Although our protocol employs enzymatic treatments, the efficiency of the enzymatic treatments does not affect the subtraction efficiency. This new subtractive enrichment method was applied to isolate Chinese cabbage defense-related genes induced by Pseudomonas syringae pv. tomato (Pst), which elicits a hypersensitive response in Chinese cabbage. After two or three rounds of subtractive hybridization, the sequences of enriched DNAs were determined and examined by BLAST analysis. Northern blot hybridization showed that 12 of the 19 genes analyzed were strongly induced by Pst treatment. Among the 12 Pst-induced genes five represent pathogenesis-related genes encoding PR1a, two chitinases, a thaumatin-like protein, and a PR4 protein. Other Pst-induced genes include two cytochrome P450 genes responsible for glucosinolate biosynthesis, a disease resistance gene homolog, and several genes encoding proteins with unknown functions.
    Biochemical and Biophysical Research Communications 01/2003; 299(3):352-9. · 2.28 Impact Factor
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    ABSTRACT: Apoptosis is a common mode of programmed cell death in multicellular organisms. However, the recent observation of yeast cell death displaying the morphology of apoptosis has suggested the presence of an ancestral cell death machinery. Here we examined apoptotic features induced by reactive oxygen species (ROS) in yeast. Saccharomyces cerevisiae show typical apoptotic features upon exposure to ROS: membrane staining with annexin V and DNA fragmentation by the TUNEL assay. The detection of apoptotic features in yeast strongly support the existence of molecular machinery performing the basic pathways of apoptosis. The phosphoinositide 3-OH kinase (PI3K)/protein kinase B (PKB) signaling pathway has been shown to prevent apoptosis in a variety of cells. It is therefore of interest to determine whether the PI3K/PKB signaling pathway is capable of protecting yeast from apoptosis induced by ROS. We determined that PI3K/PKB is capable of significantly inhibiting ROS-evoked apoptosis in yeast. These results suggest that yeast may provide a suitable model system in which to study the apoptotic signaling pathway elicited by a variety of stimuli.
    Journal of Biochemistry 06/2002; 131(5):693-9. · 3.07 Impact Factor
  • Hong Nam Kim, Jae Soon Cha, Hak Yong Kim
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    ABSTRACT: The response of plants to pathogens and wounding is dependent upon very sensitive perception mechanisms. Although genetic approaches have revealed a variety of resistance genes that activate common defense responses, defense‐related proteins are not well characterized in plants. Therefore, we used a proteomic approach to determine which defense‐related proteins are induced by salicylic acid (SA) and wounding in Chinese cabbage. We found that SA and wounding induce pathogenesis‐related protein 1a (PR1a) at both protein and mRNA levels using proteomics and Northern blot analysis, respectively. This indicates that our proteomic approach is useful for identifying defense‐related proteins. We also identified several other proteins that are induced by SA or wounding. Among the seven SA‐induced proteins identified, four may be defense‐related, including defense‐related protein, phospholipase D (PLD), resistance protein RPS2 homolog, and L‐ascorbate peroxidase. Out of the six wounding‐induced proteins identified, three may be defense‐related: heat shock cognate protein 70 (HSC70), polygalacturonase, and peroxidase P7. The precise functions of these proteins in plant defense responses await further study. However, identification of the defense‐related proteins described in this study should allow us to better understand the mechanisms and signal transduction pathways involved in defense responses in Chinese cabbage.