• Bulletin of the Korean Chemical Society
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• v.19 no.1
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• pp.110-114
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• 1998

The hydrogen-bonding interactions between thioacetamide (TA) and urea derivatives such as tetramethylurea (TMU) and dimethyldiphenylurea (DMDPU) have been studied using near-infrared absorption spectroscopy. Thermodynamic parameters for the interactions between TA and urea derivatives were determined by analyzing the $v^{as}_{N-H}$+Amide Ⅱ combination band of TA at 1970 nm. The ΔH° values, indicating the intrinsic strength of hydrogen bonding, are - 23.0 kJ/mole and - 19.8 kJ/mol for TMU and DMDPU, respectively. This is well explained by the inductive effects of substituents. Ab initio molecular orbital calculations for the proton affinity of TMU, N,N-dimethylformamide (DMF), and N,N-dimethylacetamide (DMA) in gas phase have been carried out at HF/3-21G ad HF/6-31G(d) levels, showing that the proton affinity of TMU is larger than that of DMA, which agrees well the experimental results.

• Molecules and Cells
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• v.44 no.12
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• pp.883-892
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• 2021

Genome-wide chromosome conformation capture (3C)-based high-throughput sequencing (Hi-C) has enabled identification of genome-wide chromatin loops. Because the Hi-C map with restriction fragment resolution is intrinsically associated with sparsity and stochastic noise, Hi-C data are usually binned at particular intervals; however, the binning method has limited reliability, especially at high resolution. Here, we describe a new method called HiCORE, which provides simple pipelines and algorithms to overcome the limitations of single-layered binning and predict core chromatin regions with three-dimensional physical interactions. In this approach, multiple layers of binning with slightly shifted genome coverage are generated, and interacting bins at each layer are integrated to infer narrower regions of chromatin interactions. HiCORE predicts chromatin looping regions with higher resolution, both in human and Arabidopsis genomes, and contributes to the identification of the precise positions of potential genomic elements in an unbiased manner.

• Proceedings of the Korean Vacuum Society Conference
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• 2015.08a
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• pp.64-64
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• 2015

Control of plasma processing methodologies can only occur by obtaining a thorough understanding of the physical and chemical properties of plasmas. However, all plasma processes are currently used in the industry with an incomplete understanding of the coupled chemical and physical properties of the plasma involved. Thus, they are often 'non-predictive' and hence it is not possible to alter the manufacturing process without the risk of considerable product loss. Only a more comprehensive understanding of such processes will allow models of such plasmas to be constructed that in turn can be used to design the next generation of plasma reactors. Developing such models and gaining a detailed understanding of the physical and chemical mechanisms within plasma systems is intricately linked to our knowledge of the key interactions within the plasma and thus the status of the database for characterizing electron, ion and photon interactions with those atomic and molecular species within the plasma and knowledge of both the cross-sections and reaction rates for such collisions, both in the gaseous phase and on the surfaces of the plasma reactor. The compilation of databases required for understanding most plasmas remains inadequate. The spectroscopic database required for monitoring both technological and fusion plasmas and thence deriving fundamental quantities such as chemical composition, neutral, electron and ion temperatures is incomplete with several gaps in our knowledge of many molecular spectra, particularly for radicals and excited (vibrational and electronic) species. However, the compilation of fundamental atomic and molecular data required for such plasma databases is rarely a coherent, planned research program, instead it is a parasitic process. The plasma community is a rapacious user of atomic and molecular data but is increasingly faced with a deficit of data necessary to both interpret observations and build models that can be used to develop the next-generation plasma tools that will continue the scientific and technological progress of the late 20th and early 21st century. It is therefore necessary to both compile and curate the A&M data we do have and thence identify missing data needed by the plasma community (and other user communities). Such data may then be acquired using a mixture of benchmarking experiments and theoretical formalisms. However, equally important is the need for the scientific/technological community to recognize the need to support the value of such databases and the underlying fundamental A&M that populates them. This must be conveyed to funders who are currently attracted to more apparent high-profile projects.

• Bulletin of the Korean Chemical Society
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• v.33 no.3
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• pp.869-880
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• 2012

Identification of the selective chemical features for Aurora-B inhibitors gained much attraction in drug discovery for the treatment of cancer. Hence to identify the Aurora-B critical features various techniques were utilized such as pharmacophore generation, virtual screening, homology modeling, molecular dynamics, and docking. Top ten hypotheses were generated for Aurora-B and Aurora-A. Among ten hypotheses, HypoB1 and HypoA1 were selected as a best hypothesis for Aurora-B and Aurora-A based on cluster analysis and ranking score, respectively. Test set result revealed that ring aromatic (RA) group in HypoB1 plays an essential role in differentiates Aurora-B from Aurora-A inhibitors. Hence, HypoB1 used as 3D query in virtual screening of databases and the hits were sorted out by applying drug-like properties and molecular docking. The molecular docking result revealed that 15 hits have shown strong hydrogen bond interactions with Ala157, Glu155, and Lys106. Hence, we proposed that HypoB1 might be a reasonable hypothesis to retrieve the structurally diverse and selective leads from various databases to inhibit Aurora-B.

• International Journal of Oral Biology
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• v.37 no.4
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• pp.181-188
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• 2012

As the demand for large-scale analysis of gene expression using DNA arrays increases, the importance of the surface characterization of DNA arrays has emerged. We compared the efficiency of molecular biological applications on solid-phases with different surface polarities to identify the most optimal conditions. We employed thiol-gold reactions for DNA immobilization on solid surfaces. The surface polarity was controlled by creating a self-assembled monolayer (SAM) of mercaptohexanol or hepthanethiol, which create hydrophilic or hydrophobic surface properties, respectively. A hydrophilic environment was found to be much more favorable to solid-phase molecular biological manipulations. A SAM of mercaptoethanol had the highest affinity to DNA molecules in our experimetns and it showed greater efficiency in terms of DNA hybridization and polymerization. The optimal DNA concentration for immobilization was found to be 0.5 ${\mu}M$. The optimal reaction time for both thiolated DNA and matrix molecules was 10 min and for the polymerase reaction time was 150 min. Under these optimized conditions, molecular biology techniques including DNA hybridization, ligation, polymerization, PCR and multiplex PCR were shown to be feasible in solid-state conditions. We demonstrated from our present analysis the importance of surface polarity in solid-phase molecular biological applications. A hydrophilic SAM generated a far more favorable environment than hydrophobic SAM for solid-state molecular techniques. Our findings suggest that the conditions and methods identified here could be used for DNA-DNA hybridization applications such as DNA chips and for the further development of solid-phase genetic engineering applications that involve DNA-enzyme interactions.

• Molecular & Cellular Toxicology
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• v.3 no.1
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• pp.36-45
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• 2007

Several features of the implant surface, such as topography, roughness, and composition play a relevant role in implant integration with bone. This study was conducted in order to determine the effects of different-coatings on Ti surfaces on the biological responses of a human osteoblast-like cell line (MG63). MG63 cells were cultured on HA (Hydroxyapatite coating on Titanium), Ano (HA coating on anodized surface Titanium), Zr (zirconium-coating on Titanium), and control (non-coating on Titanium). The morphology of these cells was assessed by SEM. The cDNAs prepared from the total RNAs of the MG63 were hybridized into a human cDNA microarray (1,152 elements). The appearances of the surfaces observed by SEM were different on each of the three dental substrate types. MG63 cells cultured on HA, Ano, Zr, and control exhibited cell-matrix interactions. In the expression of several genes were up-, and down-regulated on the different surfaces. The attachment and expression of key osteogenic regulatory genes were enhanced by the surface morphology of the dental materials used.

• BMB Reports
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• v.46 no.12
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• pp.594-599
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• 2013

The anti-inflammatory activity of eriodictyol and its mode of action were investigated. Eriodictyol suppressed tumor necrosis factor (mTNF)-${\alpha}$, inducible nitric oxide synthase (miNOS), interleukin (mIL)-6, macrophage inflammatory protein (mMIP)-1, and mMIP-2 cytokine release in LPS-stimulated macrophages. We found that the anti-inflammatory cascade of eriodictyol is mediated through the Toll-like Receptor (TLR)4/CD14, p38 mitogen-activated protein kinases (MAPK), extracellular-signal-regulated kinase (ERK), Jun-N terminal kinase (JNK), and cyclooxygenase (COX)-2 pathway. Fluorescence quenching and saturation-transfer difference (STD) NMR experiments showed that eriodictyol exhibits good binding affinity to JNK, $8.79{\times}10^5M^{-1}$. Based on a docking study, we propose a model of eriodictyol and JNK binding, in which eriodictyol forms 3 hydrogen bonds with the side chains of Lys55, Met111, and Asp169 in JNK, and in which the hydroxyl groups of the B ring play key roles in binding interactions with JNK. Therefore, eriodictyol may be a potent anti-inflammatory inhibitor of JNK.

• Molecular & Cellular Toxicology
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• v.1 no.4
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• pp.237-247
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• 2005

Several features of the implant surface, such as roughness, topography, and composition play a relevant role in implant integration with bone. This study was conducted in order to determine the effects of various thin layer hydroxyapatite (HA) coatings on anodized Ti surfaces on the biological responses of a human osteoblast-like cell line (MG63). MG63 cells were cultured on A (100 nm HA coating on anodized surface), B (500-700 nm HA coating on anodized surface), C ($1{\mu}m$ HA coating on anodized surface), and control (non HA coating on anodized surface) Ti. The morphology of these cells was assessed by SEM. The cDNAs prepared from the total RNAs of the MG63 were hybridized into a human cDNA microarray (1,152 elements). The appearances of the surfaces observed by SEM were different on each of the four dental substrate types. MG63 cells cultured on A, C and control exhibited cell-matrix interactions. It was B surface showing cell-cell interaction. In the expression of several genes were up-, and down-regulated on the different surfaces. The attachment and expression of key osteogenic regulatory genes were enhanced by the surface morphology of the dental materials used.

• Molecules and Cells
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• v.39 no.4
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• pp.316-321
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• 2016

The receptor activator of nuclear factor ${\kappa}B$ (RANK) and its ligand RANKL are key regulators of osteoclastogenesis and well-recognized targets in developing treatments for bone disorders associated with excessive bone resorption, such as osteoporosis. Our previous work on the structure of the RANK-RANKL complex revealed that Loop3 of RANK, specifically the non-canonical disulfide bond at the tip, performs a crucial role in specific recognition of RANKL. It also demonstrated that peptide mimics of Loop3 were capable of interfering with the function of RANKL in osteoclastogenesis. Here, we reported the structure-based design of a smaller peptide with enhanced inhibitory efficiency. The kinetic analysis and osteoclast differentiation assay showed that in addition to the sharp turn induced by the disulfide bond, two consecutive arginine residues were also important for binding to RANKL and inhibiting osteoclastogenesis. Docking and molecular dynamics simulations proposed the binding mode of the peptide to the RANKL trimer, showing that the arginine residues provide electrostatic interactions with RANKL and contribute to stabilizing the complex. These findings provided useful information for the rational design of therapeutics for bone diseases associated with RANK/RANKL function.

• Nuclear Medicine and Molecular Imaging
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• v.42 no.1
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• pp.1-7
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• 2008

PET allows non-invasive, quantitative and repetitive imaging of biological function in living animals. Small animal PET imaging with $[^{18}F]$FDG has been successfully applied to investigation of metabolism, receptor-ligand interactions, gene expression, adoptive cell therapy and somatic gene therapy. Experimental condition of animal handling impacts on the biodistribution of $[^{18}F]$FDG in small animal study. The small animal PET and CT images were registered using the hardware fiducial markers and small animal contour point. Tumor imaging in small animal with small animal $[^{18}F]$FDG PET should be considered fasting, warming, and isoflurane anesthesia level. Registered imaging with small animal PET and CT image could be useful for the detection of tumor. Small animal experimental condition of animal handling and registration method will be of most importance for small lesion detection of metastases tumor model.