• Plant Breeding and Biotechnology
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• v.5 no.4
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• pp.269-281
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• 2017

With the continual development of genetically modified (GM) crops, it has become necessary to develop detailed and effective molecular characterization methods to select candidate events from a large pool of transformation events. Relative to traditional molecular analysis methods such as the polymerase chain reaction (PCR) and Southern blot hybridization, next generation sequencing (NGS) technology for whole-genome sequencing of complex crop genomes had proven comparatively useful for in-depth molecular characterization. In this study, four transformation events, including one in Bacillus thuringiensis (Bt)-resistant rice, one in resveratrol-producing rice, and two in beta-carotene-enhanced soybeans, were selected for molecular characterization. To merge NGS analysis and Southern blot-hybridization results, we confirmed the transgene insertion sites, insertion construction, and insertion numbers of these four transformation events. In addition, the read-coverage depth assessed by NGS analysis for inserted genes might provide consistent results in terms of inserted T-DNA numbers in case of complex insertion structures and highly duplicated donor genomes; however, PCR-based methods can produce incorrect conclusions. Our combined method provides an effective and complete analytical approach for whole-genome visual inspection of transformation events that require biosafety assessment.

• Journal of Animal Reproduction and Biotechnology
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• v.37 no.3
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• pp.162-168
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• 2022

Mecoprop-p, a chlorophenoxy herbicide, has been widely used since the 1980s. Due to its high water solubility, it could be detected in the aquatic environment, as it has already been detected in the surface water or groundwater in several countries. The toxicity of other chlorophenoxy herbicides has been reported; however, there are few studies on the toxicity of mecoprop-p, one of the chlorophenoxy herbicides, on aquatic organisms. Here, we investigated the toxic effects of mecoprop-p using zebrafish. After mecoprop-p exposure, we observed that the zebrafish larvae eyes did not form normally, heart edema was generated, and the body length was shortened. The number of cells undergoing apoptosis also increased in the anterior part including head, heart, and yolk sac of the mecoprop-p-treated zebrafish compared to the untreated controls. Moreover, cardiovascular structures, including the heart and aortic arches, were also malformed after exposure to mecoprop-p. Therefore, our results suggest that mecoprop-p could cause abnormal development in zebrafish larvae and there is also a high possibility that mecoprop-p would be toxic to other aquatic organisms.

• The Bulletin of The Korean Astronomical Society
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• v.45 no.1
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• pp.41.1-41.1
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• 2020

Different molecular lines trace different physical environments (with various densities and temperatures) within molecular clouds (MCs). Therefore, multimolecular line observations are crucial to study the physical and chemical structures of MCs. We observed the Orion A and Ophiuchus clouds in six different molecular lines as a Taeduk Radio Astronomy Observatory Key Science Program (TRAO-KSP), "mapping Turbulent properties In star-forming MolEcular clouds down to the Sonic scale" (TIMES; PI: Jeong-Eun Lee). Here, we investigate the characteristic relations between the observed lines by performing the Principal Component Analysis (PCA). We also investigate the correlation between the line intensity distributions and the physical parameters, such as the gas column density and dust temperature. Finally, we will discuss how the correlations among different chemical tracers vary with the star formation environments.

• Korean Journal of Crystallography
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• v.11 no.1
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• pp.22-27
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• 2000

The structure of cis-(malonato)[(4R,5R)-4,5-bis(aminomethyl)-2-isopropyl-1,3-dioxolane]platinum(II) with a potent anticancer activity has been determined by the X-ray crystallographic method. Crystal data are as follows: Pt(C/sub 11/H/sub 20/N₂O/sub 6/), M/sub 4/=471.38, monoclinic, P2₁, a=7.112(1), b=33.615(3), c=7.135(1)Å, β=116.80(1)°, V=1522.6(3)Å, and Z=4. The two independent molecules with very similar structures are approximately related by pseudo two-fold screw axis symmetry, which makes the monolinic cell look like the orthorhombic cell with one molecule in the asymmetric unit and space group C222₁. The crystal packing mode is similar to that of the analogue with the dimethyl substituents instead of the isopropyl group. The Pt atom is coordinate to two O and two N atoms in a square planar structure. The six-membered chelate ring in the leaving ligand assumes a conformation intermediate between the half chair and the boat forms. The seven-membered ring in the carrier ligand assumes a twist-chair conformation and the oxolane ring assumes an envelope conformation. Crystal packing consists of the extensive hydrogen-bonding network in the two-dimensional molecular layers and weak van der Waals interactions between these layers.

• Asian Pacific Journal of Cancer Prevention
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• v.16 no.17
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• pp.7409-7414
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• 2015

Loop-mediated isothermal amplification (LAMP) developed by Notomi et al. (2000) has made it possible to amplify DNA with high specificity, efficiency and rapidity under isothermal conditions. The ultimate products of LAMP are stem-loop structures with several inverted repeats of the target sequence and cauliflower-like patterns with multiple loops shaped by annealing between every other inverted repeats of the amplified target in the similar strand. Because the amplification process in LAMP is achieved by using four to six distinct primers, it is expected to amplify the target region with high selectivity. However, evaluation of reaction accuracy or quantitative inspection make it necessary to append other procedures to scrutinize the amplified products. Hitherto, various techniques such as turbidity assessment in the reaction vessel, post-reaction agarose gel electrophoresis, use of intercalating fluorescent dyes, real-time turbidimetry, addition of cationic polymers to the reaction mixture, polyacrylamide gel-based microchambers, lateral flow dipsticks, fluorescence resonance energy transfer (FRET), enzyme-linked immunosorbent assays and nanoparticle-based colorimetric tests have been utilized for this purpose. In this paper, we reviewed the best-known techniques for evaluation of LAMP amplicons and their applications in molecular biology beside their advantages and deficiencies. Regarding the properties of each technique, the development of innovative prompt, cost-effective and precise molecular detection methods for application in the broad field of cancer research may be feasible.

• BMB Reports
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• v.36 no.6
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• pp.603-607
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• 2003

Abstract Plant lipid transfer proteins (LTPs) are a class of proteins whose functions are still unknown. Some are proposed to have antimicrobial activities. To understand whether LTP110, a rice LTP that we previously identified from rice leaves, plays a role in the protection function against some serious rice pathogens, we investigated the antifungal and antibacterial properties of LTP110. A cDNA sequence, encoding the mature peptide of LTP110, was cloned into the Impact-CN prokaryotic expression system. The purified protein was used for an in vitro inhibition test against rice pathogens, Pyricularia oryzae and Xanthomonas oryzae. The results showed that LTP110 inhibited the germination of Pyricularia oryzae spores, and its inhibitory activity decreased in the presence of a divalent cation. This suggests that the antifungal activity is affected by ions in the media; LTP110 only slightly inhibited the growth of Xanthomonas oryzae. However, the addition of LTP110 to cultured Chinese hamster ovarian cells did not retard growth, suggesting that the toxicity of LTP110 is only restricted to some cell types. Its antimicrobial activity is potentially due to interactions between LTP and microbe-specific structures.

• BMB Reports
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• v.48 no.7
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• pp.413-418
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• 2015

DEPDC1 is a recently identified novel tumor-related gene that is upregulated in several types of cancer and contributes to tumorigenesis. In this study, we have investigated the expression pattern and functional implications of DEPDC1 during cell cycle progression. Expression studies using synchronized cells demonstrated that DEPDC1 is highly expressed in the mitotic phase of the cell cycle. Immunofluorescence assays showed that DEPDC1 is predominantly localized in the nucleus during interphase and is redistributed into the whole cell upon nuclear membrane breakdown in metaphase. Subsequently, siRNA-mediated knockdown of DEPDC1 caused a significant mitotic arrest. Moreover, knockdown of DEPDC1 resulted in remarkable mitotic defects such as abnormal multiple nuclei and multipolar spindle structures accompanied by the upregulation of the A20 gene as well as several cell cycle-related genes such as CCNB1 and CCNB2. Taken together, our current observations strongly suggest that this novel cancerous gene, DEPDC1, plays a pivotal role in the regulation of proper mitotic progression. [BMB Reports 2015; 48(7): 413-418]

• Journal of the Korean Vacuum Society
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• v.15 no.3
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• pp.294-300
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• 2006

We fabricated the distributed feedback (DFB) InP/InGaAs/InP grating structures on InP (100) substrates by metal-organic chemical vapor deposition, and their structural properties were investigated by atomic force microscopy and scanning electron microscopy. Self-assembled InAs/InAlGaAs quantum dots (QDs) were grown on the InP/InGaAs/InP grating structures by molecular beam epitaxy, and their optical properties were compared with InAs/InAlGaAs QDs without grating structure. The duty of the grating structures was about 30%. The PL peak position of InAs/InAlGaAs QDs grown on the grating structure was 1605 nm, which was red-shifted by 18 nm from that of the InAs/InAlGaAs QDs without grating structure. This indicates that the formation of InAs/InAlGaAs QDs was affected by the existence of the DFB grating structures.

• Fibers and Polymers
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• v.3 no.1
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• pp.8-13
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• 2002

The effect of block sequence on the self-assembly of ABC-type triblock copolymers in the ordered state is investigated using an isothermal-isobaric molecular dynamics simulation. The block sequence has an important effect ,on the ]norphology of ABC triblock copolymers. Different morphologies are observed depending on the block sequence as well as the block composition. The triblock copolymers with the volume fraction of 1 : 1 : 1 ($f_A$=$f_B$=$f_C$= 0.33) show the three phase and four layered lamellar structures irrespective of the block sequence. The $A_{32}$$B_{16}$$C_{32}$triblock copolymer with $f_B$=0.2 shows a morphology In which cylinders of midblock B are formed at the interface between A and C lamellae, whereas the morphology of triblock copolymer $B_{16}$$C_{32}$ $A_{32}$ and $C_{32}$ $A_{32}$ $B_{16}$ show a cylindrical core-shell structure and a lamellar type morphology, respectively. The $A_{20}$$B_{40}$$C_{20}$the triblock copolymer with the block B as a major component shows a tricontinuous structure, whereas both $B_{40}$$C_{20}$$A_{20}$ and $C_{20}$$A_{20}$$B_{40}$ triblock coolymers exhibit the lamellar structures. When the block B has larger volrome fraction with $f_B$=0.75, the matrix is composed of block B, and other two blocks A and C form spherical domains.

• Bulletin of the Korean Chemical Society
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• v.23 no.2
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• pp.215-220
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• 2002

The structures of 1-fluorosilatrane and the silatranyl cation were calculated by Hartree-Fock (HF), Mofller-Plesset second order (MP2), and various density functional theory (DFT) methods using many different basis sets, demonstrating that the Si-N bonds in two species are quite different. The N${\rightarrow}$Si bond distance of 1-fluorosilatrane from the hybrid DFT calculations $({\sim}2.32{\AA})$ using the Perdew-Wang correlation functional agrees with the gas phase experimental value $(2.324{\AA})$, while other functionals yield larger distances. The MP2 bond distance (2.287${\AA}$ with 6-311$G^{\ast}$) is shorter, and the HF one (2.544 ${\AA}$ with 6-311$G^{\ast}$) larger than those of DFT calculations. The MP2 bond distance is in good agreement with experiment indicating that the electron correlations are crucial for the correct description of the N${\rightarrow}$Si interaction. The silatranyl cation is a stable local minimum on the potential energy surface in all methods employed suggesting that the cation could be a reaction intermediate. The Si-N bond length for the cation is about 1.87 ${\AA}$ for all calculations tested implying that the Si-N bond is mainly conventional. Bonding characteristics of the Si-N bond in two species derived from the natural bond orbital analysis support the above argument based on calculated bond lengths.