• Molecules and Cells
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• v.24 no.3
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• pp.416-423
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• 2007

Alterations in the glycan chains of cell surface glycoconjugates are frequently involved biological processes such as cell-cell interaction, cell migration, differentiation and development. Cultured embryonic (E18) rat cortical neurons underwent apoptosis in response to camptothecin, and lectin histochemistry showed that binding to apoptotic neurons of FITC-conjugated Maackia amurensis agglutinin (MAA), which is specific for terminal ${\alpha}2,3$-sialic acid residues, increased progressively with increasing concentrations of camptothecin. Analysis of the total proteins of apoptotic neurons by SDS-PAGE, and lectin blotting using HRP-labeled MAA, revealed that the expression of terminal ${\alpha}2,3$-sialic acid residues on an unknown protein with an apparent molecular mass of 25.6 kDa also increased in apoptotic neurons. NP-HPLC analysis of the total cellular N-glycans of normal and apoptotic neurons demonstrated that the expression of structurally simpler biantennary types of N-glycans fell by 49% during apoptosis whereas the more branched triantennary types of N-glycans with terminal sialic acid residues increased by up to 59%. These results suggest that increased surface expression of ${\alpha}2,3$-sialic acid residues and hyperglycosylation of N-glycans is a common feature of cellular responses to changes in cell physiology such as tumorigenesis and apoptosis.

• Korean journal of applied entomology
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• v.27 no.4
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• pp.211-218
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• 1988

Polyhedral proteins and the endogenous alkaline protease associated with larval-derived polyhedra of nuclear viruses isolated from Spodoptera litura, Bombyx mori, and Hyphantria cunea were investigated. Polyhedral proteins prepared under alkaline protease heat-inactivated condition were separated as one band with 31Kd in S. litura a H. cunea NpV and 30Kd in B. mori NPV by the SDS-polyacrylamide gel electroptoresis. Whereas polyhedral proteins without heat-inactivation were degraded into smaller polypeptides with a certain pattern in alkaline solution. The results of double-immunodiffusion and western blot analysis with antisera against polyhedral proteins indicated that those three polyhedral proteins had common antigenic determinants and the degradation of polyhedral proteins by alkaline protease could be confirmed.

• Journal of Plant Biotechnology
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• v.37 no.4
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• pp.483-493
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• 2010

Knock-out of a gene by insertional mutagenesis is a direct way to address its function through the mutant phenotype. Among ca. 15,000 gene-trapped Ds insertion lines of rice, we identified one line from selected sensitive lines in highly salt stress. We conducted gene tagging by TAIL-PCR, and DNA gel blot analysis from salt sensitive mutant. A gene encoding an oligopeptide transporter (OPT family) homologue was disrupted by the insertion of a Ds transposon into the OsOPT10 gene that was located shot arm of chromosome 8. The OsOPT10 gene (NP_001062118.) has 6 exons and encodes a protein (752 aa) containing the OPT family domain. RT-PCR analysis showed that the expression of OsOPT10 gene was rapidly and strongly induced by stresses such as high-salinity (250 mM), osmotic, drought, $100\;{\mu}M$ ABA. The subcellular localization assay indicated that OsOPT10 was localized specifically in the plasma membrane. Overexpression of OsOPT10 in Arabidopsis thaliana and rice conferred tolerance of transgenic plants to salt stress. Further we found expression levels of some stress related genes were inhibited in OsOPT10 transgenic plants. These results suggested that OsOPT10 might play crucial but differential roles in plant responses to various abiotic stresses.

• Molecules and Cells
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• v.41 no.12
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• pp.1052-1060
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• 2018

Triclosan (TCS) is a phenolic antimicrobial chemical used in consumer products and medical devices. Evidence from in vitro and in vivo animal studies has linked TCS to numerous health problems, including allergic, cardiovascular, and neurodegenerative disease. Using Caenorhabditis elegans as a model system, we here show that short-term TCS treatment ($LC_{50}$: ~0.2 mM) significantly induced mortality in a dose-dependent manner. Notably, TCS-induced mortality was dramatically suppressed by co-treatment with non-ionic surfactants (NISs: e.g., Tween 20, Tween 80, NP-40, and Triton X-100), but not with anionic surfactants (e.g., sodium dodecyl sulfate). To identify the range of compounds susceptible to NIS inhibition, other structurally related chemical compounds were also examined. Of the compounds tested, only the toxicity of phenolic compounds (bisphenol A and benzyl 4-hydroxybenzoic acid) was significantly abrogated by NISs. Mechanistic analyses using TCS revealed that NISs appear to interfere with TCS-mediated mortality by micellar solubilization. Once internalized, the TCS-micelle complex is inefficiently exported in worms lacking PMP-3 (encoding an ATP-binding cassette (ABC) transporter) transmembrane protein, resulting in overt toxicity. Since many EDCs and surfactants are extensively used in commercial products, findings from this study provide valuable insights to devise safer pharmaceutical and nutritional preparations.

• Journal of Microbiology and Biotechnology
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• v.29 no.3
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• pp.410-418
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• 2019

To investigate a novel ${\beta}$-glucosidase from Bifidobacterium breve ATCC 15700 (BbBgl) to produce compound K (CK) via ginsenoside $F_2$ by highly selective and efficient hydrolysis of the C-3 glycoside from ginsenoside Rd, the BbBgl gene was cloned and expressed in E. coli BL21. The recombinant BbBgl was purified by Ni-NTA magnetic beads to obtain an enzyme with specific activity of 37 U/mg protein using pNP-Glc as substrate. The enzyme activity was optimized at pH 5.0, $35^{\circ}C$, 2 or 6 U/ml, and its activity was enhanced by $Mn^{2+}$ significantly. Under the optimal conditions, the half-life of the BbBgl is 180 h, much longer than the characterized ${\beta}$-glycosidases, and the $K_m$ and $V_{max}$ values are 2.7 mM and $39.8{\mu}mol/mg/min$ for ginsenoside Rd. Moreover, the enzyme exhibits strong tolerance against high substrate concentration (up to 40 g/l ginsenoside Rd) with a molar biotransformation rate of 96% within 12 h. The good enzymatic properties and gram-scale conversion capacity of BbBgl provide an attractive method for large-scale production of rare ginsenoside CK using a single enzyme or a combination of enzymes.

• Journal of Mushroom
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• v.20 no.3
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• pp.178-182
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• 2022

Despite the long history of mushroom use, studies examining the genetic function of mushrooms and the development of new varieties via bio-molecular methods are significantly lacking compared to those examining other organisms. However, owing to recent developments, attempts have been made to use a novel gene-editing technique involving CRISPR/Cas9 technology and genetic scissors in mushroom studies. In particular, research is actively being conducted to utilize ribonucleoprotein particles (RNPs) that can be genetically edited with high efficiency without foreign gene insertion for ease of selection. However, RNPs are too large for Cas9 protein to pass through the cell membrane of the protoplasmic reticulum. Furthermore, guide RNA is unstable and can be easily decomposed, which remarkably affects gene editing efficiency. In this study, nanoparticles were used to mitigate the shortcomings of RNP-based gene editing techniques and to obtain transformants stably. We used Lentinula edodes (shiitake mushroom) Sanjo705-13 monokaryon strain, which has been successfully used in previous genome editing experiments. To identify a suitable osmotic buffer for the isolation of protoplast, 0.6 M and 1.2 M sucrose, mannitol, sorbitol, and KCl were treated, respectively. In addition, with various nanoparticle-forming materials, experiments were conducted to confirm genome editing efficiency via the formation of nanoparticles with calcium phosphate (CaP), which can be bound to Cas9 protein without any additional amino acid modification. RNPs/NP complex was successfully formed and protected nuclease activity with nucleotide sequence specificity.

• Journal of Plant Biotechnology
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• v.35 no.3
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• pp.177-183
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• 2008

Ac/Ds mutant lines of this study were transgenic rice plants, each of which harbored the maize transposable element Ds together with a GUS coding sequence under the control of a promoterless(Ds-GUS). We selected the mutants that were GUS expressed lines, because the GUS positive lines will be useful for identifying gene function in rice. One of these mutants was identified knock-out at Oszinc626(NP_001049991) gene, encoding a RING-H2 zinc-finger protein, by Ds insertion. In this mutant, while primary root development is normal, secondary root development from lateral root was very poor and seed development was incomplete compare with normal plant. RING zinc-finger proteins play important roles in the regulation of development in a variety of organisms. In the plant kingdom, a few genes encoding RING zinc-finger proteins have been documented with visible effects on plant growth and development. The consensus of the RING-H2(C3-H2-C3 type) domain for this group of protein is $Cys-X_2-Cys-X_{28}-Cys-X-His-X_2-His-X_2-Cys-X_{14}-Cys-X_2-Cys$. Oszinc626 encodes a predicted protein product of 445 amino acids residues with a molecular mass of 49 kDa, with a RING-zinc-finger motif located at the extreme end of the C-terminus. RT-PCR analysis indicated that the expression of Oszinc626 gene was induced by IAA, cold, dehydration, high-salinity and abscisic acid, but not by 2,4-D, and the transcription of Oszinc626 gene accumulated primarily in rice immature seeds, root meristem and shoots. The gene accumulation patterns were corresponded with GUS expression.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.63 no.3
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• pp.175-185
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• 2018

The aim of this study was to evaluate the variation of growth and quality characteristics in colored rice from 178 accessions and to develop useful, basic rice breeding data by classifying these germplasm characteristics via principal component (PC) analysis. The coefficient of variation of the 178colored rice accessions were the highest for panicle length (PL) and protein contents, followed by length-width ratio (LWR), 1000-grain weight (TGW), culm length (CL), and amylose contents, whereas the lowest was for the number of panicles per hill (NP), which is a yield component. The results from the PC analysis exhibited eigenvalues and contributions respective to each PC as follows: PC1, 2.06 and 29.49%; PC2, 1.31 and 18.75%; PC3, 1.21 and 17.36%; PC4, 1.01 and 14.38%. The eigenvalues of four PCs were over 1.0, and their cumulative contributions were 79.98%, which completes the necessary condition for evaluation of the 178 colored rice accessions. Cluster analysis showed cluster I as the largest, which included 79 accessions, while clusters II, III, IV, V, VI, and VII comprised 46, 19, 13, 4, 8, and 9 accessions, respectively. Moreover, dark brown accessions were dispersed in clusters I and II, and many resources of purple seed coat color were found in clusters V, VI, and VII. Particularly, cluster V had resources of only black and purple seed coat colors. Resources of cluster VII were found to have a relatively small average CL, PL, and LWR; notably, cluster V had the smallest average TGW, and cluster IV the lowest NP but the highest TGW. Finally, considering the yield potential, growth characteristics, heading stage, and color during breeding of colored rice, we obtained the following conclusions: cluster VII is suitable for breeding of colored rice; cross breeding among clusters I, II, and VII has a high yield potential; and it is possible to produce a superior color by cross breeding plants from cluster V and VI.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2005.09a
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• pp.267-271
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• 2005

The goal of data mining is to extract new and useful knowledge from large scale datasets. As the amount of available data grows explosively, it became vitally important to develop faster data mining algorithms for various types of data. Recently, an interest in developing data mining algorithms that operate on graphs has been increased. Especially, mining frequent patterns from structured data such as graphs has been concerned by many research groups. A graph is a highly adaptable representation scheme that used in many domains including chemistry, bioinformatics and physics. For example, the chemical structure of a given substance can be modelled by an undirected labelled graph in which each node corresponds to an atom and each edge corresponds to a chemical bond between atoms. Internet can also be modelled as a directed graph in which each node corresponds to an web site and each edge corresponds to a hypertext link between web sites. Notably in bioinformatics area, various kinds of newly discovered data such as gene regulation networks or protein interaction networks could be modelled as graphs. There have been a number of attempts to find useful knowledge from these graph structured data. One of the most powerful analysis tool for graph structured data is frequent subgraph analysis. Recurring patterns in graph data can provide incomparable insights into that graph data. However, to find recurring subgraphs is extremely expensive in computational side. At the core of the problem, there are two computationally challenging problems. 1) Subgraph isomorphism and 2) Enumeration of subgraphs. Problems related to the former are subgraph isomorphism problem (Is graph A contains graph B?) and graph isomorphism problem(Are two graphs A and B the same or not?). Even these simplified versions of the subgraph mining problem are known to be NP-complete or Polymorphism-complete and no polynomial time algorithm has been existed so far. The later is also a difficult problem. We should generate all of 2$^n$ subgraphs if there is no constraint where n is the number of vertices of the input graph. In order to find frequent subgraphs from larger graph database, it is essential to give appropriate constraint to the subgraphs to find. Most of the current approaches are focus on the frequencies of a subgraph: the higher the frequency of a graph is, the more attentions should be given to that graph. Recently, several algorithms which use level by level approaches to find frequent subgraphs have been developed. Some of the recently emerging applications suggest that other constraints such as connectivity also could be useful in mining subgraphs : more strongly connected parts of a graph are more informative. If we restrict the set of subgraphs to mine to more strongly connected parts, its computational complexity could be decreased significantly. In this paper, we present an efficient algorithm to mine frequent subgraphs that are more strongly connected. Experimental study shows that the algorithm is scaling to larger graphs which have more than ten thousand vertices.

• Experimental and Molecular Medicine
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• v.50 no.11
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• pp.5.1-5.14
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• 2018

Oxidative stress-induced mitochondrial dysfunction is implicated in the pathogenesis of intervertebral disc degeneration (IVDD). Sirtuin 3 (SIRT3), a sirtuin family protein located in mitochondria, is essential for mitochondrial homeostasis; however, the role of SIRT3 in the process of IVDD has remained elusive. Here, we explored the expression of SIRT3 in IVDD in vivo and in vitro; we also explored the role of SIRT3 in senescence, apoptosis, and mitochondrial homeostasis under oxidative stress. We subsequently activated SIRT3 using honokiol to evaluate its therapeutic potential for IVDD. We assessed SIRT3 expression in degenerative nucleus pulposus (NP) tissues and oxidative stress-induced nucleus pulposus cells (NPCs). SIRT3 was knocked down by lentivirus and activated by honokiol to determine its role in oxidative stress-induced NPCs. The mechanism by which honokiol affected SIRT3 regulation was investigated in vitro, and the therapeutic potential of honokiol was assessed in vitro and in vivo. We found that the expression of SIRT3 decreased with IVDD, and SIRT3 knockdown reduced the tolerance of NPCs to oxidative stress. Honokiol ($10{\mu}M$) improved the viability of NPCs under oxidative stress and promoted their properties of anti-oxidation, mitochondrial dynamics and mitophagy in a SIRT3-dependent manner. Furthermore, honokiol activated SIRT3 through the AMPK-PGC-$1{\alpha}$ signaling pathway. Moreover, honokiol treatment ameliorated IVDD in rats. Our study indicated that SIRT3 is involved in IVDD and showed the potential of the SIRT3 agonist honokiol for the treatment of IVDD.