• BMB Reports
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• v.29 no.2
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• pp.175-179
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• 1996

Viral surface proteins are known to play an essential role in attachment of the virus particle to the host cell membrane. In case of the hepatitis B virus (HBV) several reports have described potential receptors on the target cell side, but no definite receptor protein has been isolated yet. As for the viral side, it has been suggested that the preS region of the envelope protein, especially the preS1 region, is involved in binding of HBV to the host cell. In this study, preS1 region was recombinantly expressed in the form of a maltose binding protein (MBP) fusion protein and used to identify and visualize the expression of putative HBV receptor(s) on the host cell. Using laser scanned confocal microscopy and by FACS analysis, MBP-preS1 proteins were shown to bind to the human hepatoma cell line HepG2 in a receptor-ligand specific manner. The binding kinetic of MBP-preS1 to its cellular receptor was shown to be temperature and time dependent. In cells permeabilized with Triton X-100 and treated with the fusion protein, a specific staining of the nuclear membrane could be observed. To determine the precise location of the receptor binding site within the preS1 region, several short overlapping peptides from this region were synthesized and used in a competition assay. In this way the receptor binding epitope in preS1 was revealed to be amino acid residues 27 to 51, which is in agreement with previous reports. These results confirm the significance of the preS1 region in virus attachment in general, and suggest an internalization pathway mediated by direct attachment of the viral particle to the target cell membrane.

• The Journal of the Korea Contents Association
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• v.15 no.10
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• pp.616-625
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• 2015

Currently, oriental medicine research is focused with modern research technology and validate it's various biochemical effect by combining with molecular biology technology. But there are few searching system for finding biochemical mechanism which is related to major compounds in oriental medicine. In this research, we aimed developing korean herb database based on text-mining system by analyzing PubMed data. We have developed prototype system for searching chemical, gene and biological relation in oriental medicine. It is characterized by modern oriental medicine research trend with major chemical, gene and protein information. Analysis results can be searched on the prototype system with visualization of the biological interactions.

• Molecular & Cellular Toxicology
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• v.3 no.3
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• pp.208-213
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• 2007

With the help of a development and popularization of microarray technology that enable to us to simultaneously investigate the expression pattern of thousands of genes, the toxicogenomics experimenters can interpret the genome-scale interaction between genes exposed in toxicant or toxicant-related environment. The ultimate and primary goal of toxicogenomics identifies functional context among the group of genes that are differentially or similarly coexpressed under the specific toxic substance. On the other side, public reference databases with transcriptom, proteom, and biological pathway information are needed for the analysis of these complex omics data. However, due to the heterogeneous and independent nature of these databases, it is hard to individually analyze a large omics annotations and their pathway information. Fortunately, several web sites of the public database provide information linked to other. Nevertheless it involves not only approriate information but also unnecessary information to users. Therefore, the systematically integrated database that is suitable to a demand of experimenters is needed. For these reasons, we propose SOP (Search of Omics Pathway) database system which is constructed as the integrated biological database converting heterogeneous feature of public databases into combined feature. In addition, SOP offers user-friendly web interfaces which enable users to submit gene queries for biological interpretation of gene lists derived from omics experiments. Outputs of SOP web interface are supported as the omics annotation table and the visualized pathway maps of KEGG PATHWAY database. We believe that SOP will appear as a helpful tool to perform biological interpretation of genes or proteins traced to omics experiments, lead to new discoveries from their pathway analysis, and design new hypothesis for a next toxicogenomics experiments.

• Molecules and Cells
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• v.39 no.2
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• pp.119-128
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• 2016

Angelica polymorpha Maxim root extract (APRE) is a popular herbal medicine used for treating stomachache, abdominal pain, stomach ulcers, and rheumatism; however the effect of APRE on cancer cells has not yet been explored. Here, we examined APRE cytotoxicity seen on target neuroblastoma cells (NB) using cell viability assays, DAPI visualization of fragmented DNA, and Western blotting analysis of candidate signaling pathways involved in proliferation and apoptosis. We demonstrated that APRE reduced cell viability in NB to a greater extent than in fibroblast cells. In addition, we found that APRE could inhibit the three classes of MAPK proteins and could also down-regulate the PI3K/AKT/GSK-$3{\beta}$ activity all being relevant for proliferation and survival. APRE could also up-regulate Bax expression and down-regulate Bcl-2 and Mcl-1. With APRE treatment, depolarization of mitochondria membrane potential and activation of caspase-3 was demonstrated in the SH-SY5Y cells. We could not found increased activity of death receptor and caspase-8 as markers of the extrinsic apoptosis pathway for the APRE treated cells. In presence of a caspase-3 siRNA and a pan-caspase inhibitor, APRE could not reduce the viability of NB cells to a significant degree. So we predicted that with APRE, the intrinsic pathway was solely responsible for inducing apoptosis as we also showed that the non-caspase autophagy pathway or ER stress-ROS mediated pathways were not involved. These findings demonstrate that an intrinsic mitochondria-mediated apoptosis pathway mediates the apoptotic effects of APRE on SH-SY5Y cells, and that APRE shows promise as a novel agent for neuroblastoma therapy.

• The Plant Pathology Journal
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• v.32 no.4
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• pp.300-310
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• 2016

Pathogen infection in plants induces complex responses ranging from gene expression to metabolic processes in infected plants. In spite of many studies on biotic stress-related changes in host plants, little is known about the metabolic and phenotypic responses of the host plants to Pseudomonas cichorii infection based on image-based analysis. To investigate alterations in tomato plants according to disease severity, we inoculated plants with different cell densities of P. cichorii using dipping and syringe infiltration methods. High-dose inocula (${\geq}10^6cfu/ml$) induced evident necrotic lesions within one day that corresponded to bacterial growth in the infected tissues. Among the chlorophyll fluorescence parameters analyzed, changes in quantum yield of PSII (${\Phi}PSII$) and non-photochemical quenching (NPQ) preceded the appearance of visible symptoms, but maximum quantum efficiency of PSII ($F_v/F_m$) was altered well after symptom development. Visible/near infrared and chlorophyll fluorescence hyperspectral images detected changes before symptom appearance at low-density inoculation. The results of this study indicate that the P. cichorii infection severity can be detected by chlorophyll fluorescence assay and hyperspectral images prior to the onset of visible symptoms, indicating the feasibility of early detection of diseases. However, to detect disease development by hyperspectral imaging, more detailed protocols and analyses are necessary. Taken together, change in chlorophyll fluorescence is a good parameter for early detection of P. cichorii infection in tomato plants. In addition, image-based visualization of infection severity before visual damage appearance will contribute to effective management of plant diseases.

• Korean Journal of Oriental Medicine
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• v.17 no.3
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• pp.77-85
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• 2011

Objectives : The purpose of this study was to develop a simulator which can analyze the anti-inflammatory effects of medical herbs based on e-cell concerning p38 MAPK signal pathway. Methods : We collected data concerning medical herbs with anti-inflammatory effects and the active compounds to provide as a fundamental databse and to validate the newly developed algorithm. At this time, we used the target database as pubmed and gathered the data by data mining tool, pathway studio. Also we have developed the web-based search system for confirming database related to anti-inflammation. We researched the mechanism of actions of proteins in p38 MAPK signal pathway when active compound has been inserted into the network. We reduced total network into TAK-MKK3-p38 and made the two types of mathematical model about active compounds' interaction. Results & Conclusion : We constructed the database which have 69 cases of medical herbs, 71 cases of active compounds, about 8,000 cases of URL(Uniform Resource Locator) related to papers and reports. We designed the ordinary differential equations for response of TAK, MKK3, p38 in e-cell's cytosol and nucleus. We used this formular as measure whether an active compound of medicinal plants which is inputted by an user would have an anti-inflammation effects. We developed the visualization program which could show the change of concentration over time.

• Microbiology and Biotechnology Letters
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• v.23 no.3
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• pp.329-336
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• 1995

For the development of new antitumor antibiotics produced by microorganisms, Streptomyces sp. YBE-316 was isolated from soil. The productivity of the antitumor antibiotic from Streptomyces sp. YBE-316 gradually increased after 60 hours, and was maximum after 100 hours after inoculation in growth medium (2.0% sucrose, 1.0% soybean meal, 0.1% K$_{2}$HPO$_{4}$, pH 7.0) at 30$\circ$C, 150 rpm, 5 NL/min by 30 l jar fermentor. This antitumor antibiotic was present only in mycelium, and stable in pH 5.0-10.0 for 20 minutes at 100$\circ$C. Antitumor and antibiotic activities were maintained at neutral pH, and heat stability was low. This antitumor antibiotic was soluble in methanol and ethanol, and insoluble in water, ethyl acetate, chloroform, and n-hexane. This antitumor antibiotic was sequentially purified by acetone extraction from mycelium, butanol extraction, and silica gel column chromatography. Antitumor activity was low against most tested cell lines, but antibiotic activity was high and low against yeasts and bacteria, respectivelv. The visualization test showed that this antitumor antibiotic had higher hydroxyl, ketone, amino, carboxyl groups, and sugar(s) in its structure. Instrumental analyses showed that this antitumor antibiotic was a pentaene in polyene class antibiotics. In pentaene class antibiotics, this was considered as an eurocidin or capacidin type antibiotics. The molecular weight of this antitumor antibiotic was higher than 683.0 daltons, and this antitumor antibiotic might be glycosylated by other sugar(s), instead of mycosamine or perosamine, an amino sugar.

• Molecules and Cells
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• v.44 no.9
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• pp.627-636
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• 2021

The three-dimensional organization of chromatin and its time-dependent changes greatly affect virtually every cellular function, especially DNA replication, genome maintenance, transcription regulation, and cell differentiation. Sequencing-based techniques such as ChIP-seq, ATAC-seq, and Hi-C provide abundant information on how genomic elements are coupled with regulatory proteins and functionally organized into hierarchical domains through their interactions. However, visualizing the time-dependent changes of such organization in individual cells remains challenging. Recent developments of CRISPR systems for site-specific fluorescent labeling of genomic loci have provided promising strategies for visualizing chromatin dynamics in live cells. However, there are several limiting factors, including background signals, off-target binding of CRISPR, and rapid photobleaching of the fluorophores, requiring a large number of target-bound CRISPR complexes to reliably distinguish the target-specific foci from the background. Various modifications have been engineered into the CRISPR system to enhance the signal-to-background ratio and signal longevity to detect target foci more reliably and efficiently, and to reduce the required target size. In this review, we comprehensively compare the performances of recently developed CRISPR designs for improved visualization of genomic loci in terms of the reliability of target detection, the ability to detect small repeat loci, and the allowed time of live tracking. Longer observation of genomic loci allows the detailed identification of the dynamic characteristics of chromatin. The diffusion properties of chromatin found in recent studies are reviewed, which provide suggestions for the underlying biological processes.

• Journal of Microbiology and Biotechnology
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• v.33 no.8
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• pp.1101-1110
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• 2023

Streptococcus mutans is the primary causative agent of caries, which is one of the most common human diseases. Thus, rapid and early detection of cariogenic bacteria is critical for its prevention. This study investigated the combination of loop-mediated isothermal amplification (LAMP) and microfluid technology to quantitatively detect S. mutans. A low-cost, rapid microfluidic chip using LAMP technology was developed to amplify and detect bacteria at 2.2-2.2 × 10⁶ colony-forming units (CFU)/ml and its detection limits were compared to those of standard polymerase chain reaction. A visualization system was established to quantitatively determine the experimental results, and a functional relationship between the bacterial concentration and quantitative results was established. The detection limit of S. mutans using this microfluidic chip was 2.2 CFU/ml, which was lower than that of the standard approach. After quantification, the experimental results showed a good linear relationship with the concentration of S. mutans, thereby confirming the effectiveness and accuracy of the custom-made integrated LAMP microfluidic system for the detection of S. mutans. The microfluidic system described herein may represent a promising simple detection method for the specific and rapid testing of individuals at risk of caries.

• Journal of Life Science
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• v.21 no.5
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• pp.631-646
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• 2011

Mesenchymal stem cells (MSC) are multipotent and can be isolated from diverse human tissues including bone marrow, fat, placenta, dental pulp, synovium, tonsil, and the thymus. They function as regulators of tissue homeostasis. Because of their various advantages such as plasticity, easy isolation and manipulation, chemotaxis to cancer, and immune regulatory function, MSCs have been considered to be a potent cell source for regenerative medicine, cancer treatment and other cell based therapy such as GVHD. However, relating to its supportive feature for surrounding cell and tissue, it has been frequently reported that MSCs accelerate tumor growth by modulating cancer microenvironment through promoting angiogenesis, secreting growth factors, and suppressing anti-tumorigenic immune reaction. Thus, clinical application of MSCs has been limited. To understand the underlying mechanism which modulates MSCs to function as tumor supportive cells, we co-cultured human adipose tissue derived mesenchymal stem cells (ASC) with cancer cell lines H460 and U87MG. Then, expression data of ASCs co-cultured with cancer cells and cultured alone were obtained via microarray. Comparative expression analysis was carried out using DAVID (Database for Annotation, Visualization and Integrated Discovery) and PANTHER (Protein ANalysis THrough Evolutionary Relationships) in divers aspects including biological process, molecular function, cellular component, protein class, disease, tissue expression, and signal pathway. We found that cancer cells alter the expression profile of MSCs to cancer associated fibroblast like cells by modulating its energy metabolism, stemness, cell structure components, and paracrine effect in a variety of levels. These findings will improve the clinical efficacy and safety of MSCs based cell therapy.