• Journal of Life Science
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• v.27 no.6
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• pp.673-679
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• 2017

Microtubules are long rods in the cytoplasm of cells that plays a role in cell motility and intracellular transport. Microtubule-based transport by motor proteins is essential in intracellular transport. Kinesin 1 is a molecular motor protein that mediates the intracellular transport of various membranous vesicles, mRNAs, and proteins along microtubules. It is comprised of two heavy chains (KHCs, also called KIF5s) and two light chains (KLCs). KIF5s bear a motor domain in their amino (N)-terminal regions and interact with various cargoes through the cargo-binding domain in their carboxyl (C)-terminal regions. To identify proteins interacting with KIF5B, yeast two-hybrid screening was performed, and a specific interaction with the cytoplasmic linker protein 170 (CLIP-170), a plus end microtubule-binding protein, was found. The coiled-coil domain of CLIP-170 is essential for interactions with KIF5B in the yeast two-hybrid assay. CLIP-170 bound to the cargo-binding domain of KIF5B. Also, other KIF5s, KIF5A and KIF5C, interacted with CLIP-170 in the yeast two-hybrid assay. In addition, glutathione S-transferase (GST) pull-downs showed that KIF5s specifically interacted with CLIP-170. An antibody to KIF5B specifically co-immunoprecipitated CLIP-170 associated with KIF5B from mouse brain extracts. These results suggest that kinesin 1 motor protein may transport CLIP-170 in cells.

• Proceedings of the Korean Vacuum Society Conference
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• 2011.02a
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• pp.407-408
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• 2011

Natural boron consists of two stable isotopes 10B and 11B with natural abundance of 18.8 atom percent of 10B and 81.2 atom percent of 11B. The thermal neutron absorption cross-section for 10B and 11B are 3837 barn and 0.005 barn respectively. 10B enriched specific compounds are used for control rods and as a reactor coolant additives. In this work 2 methods for boron enrichment were analysed: 1) Gas irradiation in static conditions. Dissociation occurs due to multiphoton absorption by specific isotopes in appropriately tuned laser field. IR shifted laser pulses are usually used in combination with increasing the laser intensity also improves selectivity up to some degree. In order to prevent recombination of dissociated molecules BCl3 is mixed with H2S 2) SILARC method. Advantages of this method: a) Gas cooling is helpful to split and shrink boron isotopes absorption bands. In order to achieve better selectivity BCl3 gas has to be substantially rarefied (~0.01%-5%) in mixture with carrier gas. b) Laser intensity is lower than in the first method. Some preliminary calculations of dissociation and recombination with carrier gas molecules energetics for both methods will be demonstrated Boron separation in SILARC method can be represented as multistage process: 1) Mixture of BCl3 with carrier gas is putted in reservoir 2) Gas overcooling due to expansion through Laval nozzle 3) IR multiphoton absorption by gas irradiated by specifically tuned laser field with subsequent gradual gas condensation in outlet chamber It is planned to develop software which includes these stages. This software will rely on the following available software based on quantum molecular dynamics in external quantized field: 1) WavePacket: Each particle is treated semiclassicaly based on Wigner transform method 2) Turbomole: It is based on local density methods like density of functional methods (DFT) and its improvement- coupled clusters approach (CC) to take into account quantum correlation. These models will be used to extract information concerning kinetic coefficients, and their dependence on applied external field. Information on radiative corrections to equation of state induced by laser field which take into account possible phase transition (or crossover?) can be also revealed. This mixed phase equation of state with quantum corrections will be further used in hydrodynamical simulations. Moreover results of these hydrodynamical simulations can be compared with results of CFD calculations. The first reasonable question to ask before starting the CFD simulations is whether turbulent effects are significant or not, and how to model turbulence? The questions of laser beam parameters and outlet chamber geometry which are most optimal to make all gas volume irradiated is also discussed. Relationship between enrichment factor and stagnation pressure and temperature based on experimental data is also reported.

• Journal of the Computational Structural Engineering Institute of Korea
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• v.27 no.3
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• pp.137-145
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• 2014

We present a design sensitivity analysis(DSA) method for multiscale problems based on bridging scale decomposition. In this paper, we utilize a bridging scale method for the coupled system analysis. Since the analysis of full MD systems requires huge amount of computational costs, a coupled system of MD-level and continuum-level simulation is usually preferred. The information exchange between the MD and continuum levels is taken place at the MD-continuum boundary. In the bridging scale method, a generalized Langevin equation(GLE) is introduced for the reduced MD system and the GLE force using a time history kernel is applied at the boundary atoms in the MD system. Therefore, we can separately analyze the MD and continuum level simulations, which can accelerate the computing process. Once the simulation of coupled problems is successful, the need for the DSA is naturally arising for the optimization of macro-scale design, where the macro scale performance of the system is maximized considering the micro scale effects. The finite difference sensitivity is impractical for the gradient based optimization of large scale problems due to the restriction of computing costs but the analytical sensitivity for the coupled system is always accurate. In this study, we derive the analytical design sensitivity to verify the accuracy and applicability to the design optimization of the coupled system.

• Journal of the Computational Structural Engineering Institute of Korea
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• v.25 no.4
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• pp.315-321
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• 2012

In this study, a sequential multiscale homogenization method to characterize the effective thermal conductivity of nano particulate polymer nanocomposites is proposed through a molecular dynamics(MD) simulations and a finite element-based homogenization method. The thermal conductivity of the nanocomposites embedding different-sized nanoparticles at a fixed volume fraction of 5.8% are obtained from MD simulations. Due to the Kapitza thermal resistance, the thermal conductivity of the nanocomposites decreases as the size of the embedded nanoparticle decreases. In order to describe the nanoparticle size effect using the homogenization method with accuracy, the Kapitza interface in which the temperature discontinuity condition appears and the effective interphase zone formed by highly densified matrix polymer are modeled as independent phases that constitutes the nanocomposites microstructure, thus, the overall nanocomposites domain is modeled as a four-phase structure consists of the nanoparticle, Kapitza interface, effective interphase, and polymer matrix. The thermal conductivity of the effective interphase is inversely predicted from the thermal conductivity of the nanocomposites through the multiscale homogenization method, then, exponentially fitted to a function of the particle radius. Using the multiscale homogenization method, the thermal conductivities of the nanocomposites at various particle radii and volume fractions are obtained, and parametric studies are conducted to examine the effect of the effective interphase on the overall thermal conductivity of the nanocomposites.

• The Korean Journal of Physiology and Pharmacology
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• v.16 no.6
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• pp.413-422
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• 2012

The purpose of this study is to investigated the mechanism of pharmacological action of local anesthetic and provide the basic information about the development of new effective local anesthetics. Fluorescent probe techniques were used to evaluate the effect of lidocaine HCl on the physical properties (transbilayer asymmetric lateral and rotational mobility, annular lipid fluidity and protein distribution) of synaptosomal plasma membrane vesicles (SPMV) isolated from bovine cerebral cortex, and liposomes of total lipids (SPMVTL) and phospholipids (SPMVPL) extracted from the SPMV. An experimental procedure was used based on selective quenching of 1,3-di(1-pyrenyl)propane (Py-3-Py) and 1,6-diphenyl-1,3,5-hexatriene (DPH) by trinitrophenyl groups, and radiationless energy transfer from the tryptophans of membrane proteins to Py-3-Py. Lidocaine HCl increased the bulk lateral and rotational mobility of neuronal and model membrane lipid bilayes, and had a greater fluidizing effect on the inner monolayer than the outer monolayer. Lidocaine HCl increased annular lipid fluidity in SPMV lipid bilayers. It also caused membrane proteins to cluster. The most important finding of this study is that there is far greater increase in annular lipid fluidity than that in lateral and rotational mobilities by lidocaine HCl. Lidocaine HCl alters the stereo or dynamics of the proteins in the lipid bilayers by combining with lipids, especially with the annular lipids. In conclusion, the present data suggest that lidocaine, in addition to its direct interaction with proteins, concurrently interacts with membrane lipids, fluidizing the membrane, and thus inducing conformational changes of proteins known to be intimately associated with membrane lipid.

• Proceedings of the Korean Vacuum Society Conference
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• 2010.02a
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• pp.121-121
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• 2010

ZnO is a promising material for the application of high efficiency light emitting diodes with short wavelength region for its large bandgap energy of 3.37 eV which is similar to GaN (3.39 eV) at room temperature. The large exciton binding energy of 60 meV in ZnO provide provides higher efficiency of emission for optoelectronic device applications. Several ZnO/ZnMgO multiple quantum well (MQW) structures have been grown on various substrates such as sapphire, GaN, Si, and so on. However, the achievement of high quality ZnO/ZnMgO MQW structures has been somehow limited by the use of lattice-mismatched substrates. Therefore, we propose the optical properties of ZnO/ZnMgO multiple quantum well (MQW) structures with different well widths grown on lattice-matched ZnO substrates by molecular beam epitaxy. Photoluminescence (PL) spectra show MQW emissions at 3.387 and 3.369 eV for the ZnO/ZnMgO MQW samples with well widths of 2 and 5 nm, respectively, due to the quantum confinement effect. Time-resolved PL results show an efficient photo-generated carrier transfer from the barrier to the MQWs, which leads to an increased intensity ratio of the well to barrier emissions for the ZnO/ZnMgO MQW sample with the wider width. From the power-dependent PL spectra, we observed no PL peak shift of MQW emission in both samples, indicating a negligible built-in electric field effect in the ZnO/$Zn_{0.9}Mg_{0.1}O$ MQWs grown on lattice-matched ZnO substrates.

• Bulletin of the Korean Chemical Society
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• v.7 no.5
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• pp.367-371
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• 1986

Dynamic and equilibrium properties of n-alkane chains immersed in solvent molecules have been investigated by a molecular dynamics method. The n-alkane chain is assumed to be a chain of elements (CH$_2$) interconnected by bonds having a fixed bond length and bond angle, but each bond of the chain is allowed to execute hindered internal rotation. We studied the effect of the number of the chain elements (N$_c$ = 10, 15 and 20) on the equilibrium properties of the system, e.g., the pair correlation functions between a chain element and solvent molecules, g$_{cs}$(r), and between the chain elements, g$_{cc}$(r), and the configurational properties such as the mean-square end-to-end distance < R$^2$ >, the mean-square radius of gyration < S$^2$ >, and the eigenvalues of the moment-of-inertia tensor < S$_i^2$ > / < S$^2$ > (i = 1, 2 and 3). We also studied the dynamic properties of the system, e.g., the autocorrelation function C(A;t) where A = R$^2$(t), = S$^2$(t), or = ${\vec{V}}(t)({\vec{V}}$ = velocity of the center of mass), and the diffusion coefficient D. The g$_{cs}$(r)'s are almost equal irrespective of the change of Nc while g$_{cc}$(r) becomes larger as N$_c$ increases; The MD computed configurational properties < R$^2$2 > and < S$^2$ > were found to be a little different from the values calculated from the statistical equations of < R$^2$ > and < S$^2$ >, it may be due to the fact that our model for the MD simulations includes a long-range volume effect. From the < S$_i^2$ > / < S$^2$ >, it is found that the chain molecule has a nearly spherical shape irrespective of the variation of N$_c$. For the dynamic properties we found that the C(R$^2$;t) and C(S$^2$;t) of lower N$_c$ decay faster than those of higher N$_c$, while the C($\vec V$;t) of the center of mass in the chain is weakly dependent on the N$_c$. The center of mass diffusion coefficient D$_c$ decreases as N$_c$ increases while the end point diffusion coefficient D$_e$ is nearly equal irrespective of the change of N$_c$.

• ALGAE
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• v.36 no.1
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• pp.25-36
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• 2021

The mixotrophic dinoflagellate Tripos furca causes red tides in the waters of many countries. To understand its population dynamics, mortality due to predation as well as growth rate should be assessed. Prior to the present study, the heterotrophic dinoflagellates Noctiluca scintillans, Polykrikos kofoidii, Protoperidinium steinii, and mixotrophic dinoflagellate Fragilidium subglobosum were known to ingest T. furca. However, if other common heterotrophic protists are able to feed on T. furca has not been tested. We explored interactions between T. furca and nine heterotrophic dinoflagellates and one naked ciliate. Furthermore, we investigated the abundance of T. furca and common heterotrophic protists in coastal-offshore waters off Yeosu, southern Korea, on Jul 31, 2020, during its red tide. Among the tested heterotrophic protists, the heterotrophic dinoflagellates Aduncodinium glandula, Luciella masanensis, and Pfiesteria piscicida were able to feed on T. furca. However, the heterotrophic dinoflagellates Gyrodiniellum shiwhaense, Gyrodinium dominans, Gyrodinium jinhaense, Gyrodinium moestrupii, Oblea rotunda, Oxyrrhis marina, and the naked ciliate Rimostrombidium sp. were unable to feed on it. However, T. furca did not support the growth of A. glandula, L. masanensis, or P. piscicida. Red tides dominated by T. furca prevailed in the South Sea of Korea from Jun 30 to Sep 5, 2020. The maximum abundance of heterotrophic dinoflagellates in the waters off Yeosu on Jul 31, 2020, was as low as 5.0 cells mL-1, and A. glandula, L. masanensis, and P. piscicida were not detected. Furthermore, the abundances of the known predators F. subglobosum, N. scintillans, P. kofoidii, and Protoperidinium spp. were very low or negligible. Therefore, no or low abundance of effective predators might be partially responsible for the long duration of the T. furca red tides in the South Sea of Korea in 2020.

• Journal of Life Science
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• v.33 no.8
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• pp.651-662
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• 2023

Peroxisomes, known as microbodies, are a class of morphologically similar subcellular organelles commonly found in most eukaryotic cells. They are 0.2~1.8 ㎛ in diameter and are bound by a single membrane. The matrix is usually finely granular, but occasionally crystalline or fibrillary inclusions are observed. They characteristically contain hydrogen peroxide (H₂O₂) generating oxidases and contain the enzyme catalase, thus confining the metabolism of the poisonous H₂O₂ within these organelles. Therefore, the eukaryotic organelles are greatly dynamic both in morphology and metabolism. Plant peroxisomes, in particular, are associated with numerous metabolic processes, including β-oxidation, the glyoxylate cycle and photorespiration. Furthermore, plant peroxisomes are involved in development, along with responses to stresses such as the synthesis of important phytohormones of auxins, salicylic acid and jasmonic acids. In the past few decades substantial progress has been made in the study of peroxisome biogenesis in eukaryotic organisms, mainly in animals and yeasts. Advancement of sophisticated techniques in molecular biology and widening of the range of genomic applications have led to the identification of most peroxisomal genes and proteins (peroxins, PEXs). Furthermore, recent applications of proteome study have produced fundamental information on biogenesis in plant peroxisomes, together with improving our understanding of peroxisomal protein targeting, regulation, and degradation. Nonetheless, despite this progress in peroxisome development, much remains to be explained about how peroxisomes originate from the endoplasmic reticulum (ER), then assemble and divide. Peroxisomes perform dynamic roles in many phases of plant development, and in this review, we focus on the latest progress in furthering our understanding of plant peroxisome functions, biogenesis, and dynamics.

• BMB Reports
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• v.56 no.12
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• pp.663-668
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• 2023

C-reactive protein (CRP) is an inflammatory marker and risk factor for atherosclerosis and cardiovascular diseases. However, the mechanism through which CRP induces myocardial damage remains unclear. This study aimed to determine how CRP damages cardiomyocytes via the change of mitochondrial dynamics and whether survivin, an anti-apoptotic protein, exerts a cardioprotective effect in this process. We treated H9c2 cardiomyocytes with CRP and found increased intracellular ROS production and shortened mitochondrial length. CRP treatment phosphorylated ERK1/2 and promoted increased expression, phosphorylation, and translocation of DRP1, a mitochondrial fission-related protein, from the cytoplasm to the mitochondria. The expression of mitophagy proteins PINK1 and PARK2 was also increased by CRP. YAP, a transcriptional regulator of PINK1 and PARK2, was also increased by CRP. Knockdown of YAP prevented CRP-induced increases in DRP1, PINK1, and PARK2. Furthermore, CRP-induced changes in the expression of DRP1 and increases in YAP, PINK1, and PARK2 were inhibited by ERK1/2 inhibition, suggesting that ERK1/2 signaling is involved in CRP-induced mitochondrial fission. We treated H9c2 cardiomyocytes with a recombinant TAT-survivin protein before CRP treatment, which reduced CRP-induced ROS accumulation and reduced mitochondrial fission. CRP-induced activation of ERK1/2 and increases in the expression and activity of YAP and its downstream mitochondrial proteins were inhibited by TAT-survivin. This study shows that mitochondrial fission occurs during CRP-induced cardiomyocyte damage and that the ERK1/2-YAP axis is involved in this process, and identifies that survivin alters these mechanisms to prevent CRP-induced mitochondrial damage.