• 한국생물정보학회:학술대회논문집
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• 한국생물정보시스템생물학회 2005년도 BIOINFO 2005
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• pp.313-318
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• 2005

Estimating the reliability of protein-protein interaction data sets obtained by high-throughput technologies such as yeast two-hybrid assays and mass spectrometry is of great importance. We develop a maximum likelihood estimation method that uses both protein localization and gene expression data to estimate the reliability of protein interaction data sets. By integrating protein localization data and gene expression data, we can obtain more accurate estimates of the reliability of various interaction data sets. We apply the method to protein physical interaction data sets and protein complex data sets. The reliability of the yeast two-hybrid interactions by Ito et al. (2001) is 27%, and that by Uetz et at.(2000) is 68%. The reliability of the protein complex data sets using tandem affinity purification-mass spec-trometry (TAP) by Gavin et at. (2002) is 45%, and that using high-throughput mass spectrometric protein complex identification (HMS-PCI) by Ho et al. (2002) is 20%. The method is general and can be applied to analyze any protein interaction data sets.

• Journal of Microbiology and Biotechnology
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• 제20권9호
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• pp.1283-1287
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• 2010

In eukaryotes, eRF3 participates in translation termination and belongs to the superfamily of GTPases. In this work, the dissociation constants for nucleosides bound to Euplotes octocarinatus eRF3 in the presence and absence of eRF1a were determined using fluorescence spectra methods. Furthermore, a GTP hydrolyzing assay of eRF3 was carried out using an HPLC method, and the kinetic parameters for GTP hydrolysis by eRF3 were determined. Consistent with data from humans, the results showed that eRF1a promoted the binding of GTP to eRF3 and the GTP hydrolyzing activity of eRF3. However, in contrast to the lack of GTP binding in the absence of eRF1 in human eRF3, the E. octocarinatus eRF3 was able to bind GTP by itself. The nucleotide binding affinity of the E. octocarinatus eRF3 also differed from the human data. A structure model and amino acid sequence alignment of potential G domains indicated that these differences may be due to valine 317 and glutamate 452 displacing the conserved glycine and lysine involved in GTP binding.

• 천문학회보
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• 제41권2호
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• pp.55.5-56
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• 2016

Turbulence plays an important role in molecular clouds. However, the properties of turbulence are poorly understood. In order to study the influence of turbulence in molecular clouds, we need to sample the turbulent properties in the full range of scales down to sonic scale. We mapped the $20^{\prime}{\times}60^{\prime}$ area covering the Orion Molecular Cloud (OMC) 1-4 region in HCN 1-0 and HCO+ 1-0 with Taeduk Radio Astronomy Observatory (TRAO) 14-m telescope as part of the TRAO key science program, "Mapping turbulent properties of star-forming molecular clouds down to the sonic scale (PI: Jeong-Eun Lee)". In addition, we combine our TRAO data with other molecular line maps ($^{13}CO$ 1-0, $C^{18}O$ 1-0, CS 1-0, $N_2H^+$ 1-0) obtained with the Nobeyama Radio Observatory (NRO) 45-m telescope. To analyze these data, we apply statistical methods, the principal component analysis (PCA) and spectral correlation function (SCF), which are known to be useful to study underlying turbulent properties and to quantitatively characterize cloud structure. We will present the preliminary results of observations and analyses.

• 천문학회보
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• 제37권1호
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• pp.41.1-41.1
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• 2012

Interactions between the galactic interstellar medium (ISM) and the intra cluster medium (ICM) are believed to be one of the main processes affecting galaxy evolution in cluster environments. The aim of our research is to study the molecular gas properties of a galaxy under the ICM pressure in the cluster environment. It has been well known that cluster galaxies are deficient in atomic hydrogen gas (HI gas) compared to their field counterparts and now there is much evidence that low density ISM is being removed by ram pressure due to ICM wind. Meanwhile, no significant molecular gas deficiency of the cluster galaxy population has been found yet they show overall lower star formation rate than galaxies in the field, and it is still puzzling how the star formation could decrease without stripping of dense molecular gas. To address this issue, we probe the detailed molecular gas properties of NGC 4402, located near the cluster center, as part of a study of four spiral galaxies in the Virgo Cluster. NGC 4402 is well known undergoing ram pressure stripping with a truncated HI disk($D_{HI}/D_{opt}$ - 0.75 and only 36% of HI gas compare to field galaxies of a similar size) and a disturbed gas morphology. Comparing the high resolution 12CO and 13CO data of NGC 4402 from the Sub Millimeter Array (SMA) with existing other wavelength data, we probe the spatial distribution and a physical condition of molecular gas under strong ICM pressure. We discuss the star formation activity might have been altered and hence how the global color of NGC4402 would change in the future.

• Advances in nano research
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• 제3권3호
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• pp.143-168
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• 2015

Initiation of crack and its growth simulation requires accurate model of traction - separation law. Accurate modeling of traction-separation law remains always a great challenge. Atomistic simulations based prediction has great potential in arriving at accurate traction-separation law. The present paper is aimed at establishing a method to address the above problem. A method for traction-separation law prediction via utilizing atomistic simulations data has been proposed. In this direction, firstly, a simpler approach of common neighbor analysis (CNA) for the prediction of crack growth has been proposed and results have been compared with previously used approach of threshold potential energy. Next, a scheme for prediction of crack speed has been demonstrated based on the stable crack growth criteria. Also, an algorithm has been proposed that utilizes a variable relaxation time period for the computation of crack growth, accurate stress behavior, and traction-separation atomistic law. An understanding has been established for the generation of smoother traction-separation law (including the effect of free surface) from a huge amount of raw atomistic data. A new curve fit has also been proposed for predicting traction-separation data generated from the molecular dynamics simulations. The proposed traction-separation law has also been compared with the polynomial and exponential model used earlier for the prediction of traction-separation law for the bulk materials.

• 천문학회보
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• 제37권2호
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• pp.85.2-85.2
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• 2012

The interstellar medium (ISM) of galaxies in the galaxy cluster can well be affected by the intracluster medium (ICM). Among many suggested environmental processes, ram pressure stripping can effectively remove gas through the interaction with the ICM. In fact, Cluster galaxies are lower in HI gas mass compared to their field counterparts, and in recent high resolution HI imaging studies, many galaxies in dense environments have been found to be ram pressure stripped in HI. However, it is still under debate whether the ICM pressure can also remove dense molecular gas from the galactic disk, which plays more important role in star formation and hence galaxy evolution. To answer this question, we have obtained high resolution 12/13 CO (2-1) data from the Sub Millimeter Array (SMA) of four galaxies at various HI stripping stages to study how the molecular gas properties change as the galaxy experiences the ICM pressure. We investigate the physical properties of molecular gas with 12/13 CO images. By comparing with other wavelength data, i.e. data(optical, HI, $H{\alpha}$, etc), we discuss how and in which timescale galaxies can migrate from the blue cloud to the red sequence due to ram pressure stripping.

• Journal of Species Research
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• 제9권1호
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• pp.46-55
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• 2020

Chrysosplenium grayanum Maxim. (Series Nepalensia), which had been known to be restricted to Japan, was newly discovered from Mt. Cheongtae in Yeonggwang-gun, Jeollanam-do, located in the southern part of the Korean Peninsula. Species identification was confirmed using morphological characteristics and DNA sequence data, while comparing with materials obtained from Japan and herbarium specimens. Chrysosplenium grayanum is clearly distinguished from the remaining taxa of the genus Chrysosplenium by having glabrous plant body, opposite leaves, cylindrical papillae with roundish head at the tip on the smooth seed surface, and four stamens. Molecular sequence data of the nuclear ribosomal ITS regions, chloroplast rbcL and matK genes strongly supported that this previously unknown Chrysosplenium species from Korea is C. grayanum. Taking the molecular and the morphological evidence into consideration, it is clear that newly discovered Chrysosplenium population in Korea is conspecific with the widely distributed C. grayanum in Japan. In this paper, we provide a description, illustration, and photo images of Chrysosplenium grayanum from Korea and also a key to the Chrysosplenium species in Korea.

• 환경생물
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• 제39권1호
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• pp.32-38
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• 2021

Cyanobium is a genus of picoprokaryotic cyanophytes, which includes species worldwide. The present study investigated the morphology, ultrastructure, and molecular phylogeny of the unrecorded genus Cyanobium Rippka & Cohen-Bazire 1983 and species Cyanobium gracile Rippka & Cohen-Bazire 1983. A C. gracile culture from a freshwater sample collected from the Adongji pond was established by single-cell isolation. Morphological data were analyzed using light and transmission electron microscopy. C. gracile lives as solitary cells without gelatinous envelopes and is ovate, oval, or shortly rod-shaped. Thylakoids are laid along the cell walls, with three thylakoid membranes parallel to each other. Nucleoplasm was observed in the center of the cell. Molecular phylogeny performed with data from 16S small subunit ribosomal DNA gene (SSU rDNA) sequences showed that the three strains of C. gracile, including the type strain (PCC6307) and a newly recorded strain (Adong101619), formed a distinct clade with a high supporting value (maximum-likelihood=100, pp=1.00). Based on morphology and molecular data, we report the newly recorded C. gracile in Korea.

• Nuclear Engineering and Technology
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• 제55권4호
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• pp.1324-1331
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• 2023

In the present work, we carried out a molecular dynamics study of the kinetic properties of the FLiNaK molten salt, as well as a detailed study of the structure of this salt melt. The high value of the self-diffusion coefficient of fluorine ions is due to the large number of Coulomb repulsions between the most numerous negative ions. The calculated values of shear viscosity are in good agreement with the experimental data, as well as with the reference data obtained on the basis of finding the most reliable data. The total and partial functions of the radial distribution are calculated. According to the statistical analysis, fluorine ions have the greatest numerical diversity in the environment of similar ions, and sodium ions with the lowest representation in FLiNaK, have the least such diversity. For the subsystem of fluorine ions, the rotational symmetry of the fifth order is the most pronounced. Some of the fluorine ions form linear chains consisting of three atoms, which are not formed for positive ions. The results of the work give an understanding of the behavior molten FLiNaK under operating conditions in a molten salt reactor and will find application in future studies of this molten salt.

• BMB Reports
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• 제51권6호
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• pp.296-301
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• 2018

Mitochondrial DNA (mtDNA) mutations are often observed in various cancer types. Although the correlation between mitochondrial dysfunction and cancer malignancy has been demonstrated by several studies, further research is required to elucidate the molecular mechanisms underlying accelerated tumor development and progression due to mitochondrial mutations. We generated an mtDNA-depleted cell line, ${\rho}^0$, via long-term ethidium bromide treatment to define the molecular mechanisms of tumor malignancy induced by mitochondrial dysfunction. Mitochondrial dysfunction in ${\rho}^0$ cells reduced drug-induced cell death and decreased the expression of pro-apoptotic proteins including p53. The p53 expression was reduced by activation of nuclear $factor-{\kappa}B$ that depended on elevated levels of free calcium in $HCT116/{\rho}^0$ cells. Overall, these data provide a novel mechanism for tumor development and drug resistance due to mitochondrial dysfunction.