• Korean Journal of Breeding Science
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• v.42 no.1
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• pp.1-10
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• 2010

Five mutants were investigated at the molecular level to determine the factors responsible for mutated endosperm types. They were classified as high (HA) or low amylose (LA) phenotypes based on the amylose content in endosperm. The five were previously produced from Ilpum and Shindongjin cultivar treated with N-methyl-N-nitrosourea and gamma-ray irradiation, respectively. Analysis of the genomic structure and expression of Granule-bounded Starch Synthase I (GBSSI) genes revealed that mutants generally showed a higher incidence of nucleotide transition than transversion, and the $A:T{\rightarrow}G:C$ transition was particularly prevalent. The rates of nucleotide substitution in HA mutants were generally higher than those in the LA mutants, leading to higher substitutions of amino acid in the HA mutants. Neither nucleotide substitutions interfering with intron splicing or causing early termination of protein translation were found, nor any large-sized deletions or additions were found in all the mutants. In principle, amylose content can be regulated by three factors: internal alterations of GBSSI protein, the strength of gene expression, and other unknown external factors. Our results indicate that the endosperm mutants from Shindongjin arose from internal alterations of GBSSI proteins, which may be the result of amino acid substitutions. On the other hand, the Ilpum mutants might be principally caused by the alteration of gene expression level. Analysis of another three glutinous cultivars revealed that the major factor leading to glutinous phenotypes is the 23-bp duplicative motif (5'-ACGGGTTCCAGGGCCTCAAGCCC-3') commonly found in exon 2, which results in the premature termination of protein translation leading to the production of a non-functional GBSSI enzyme.

• Korean Journal of Metals and Materials
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• v.46 no.1
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• pp.6-12
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• 2008

Peptides with specific sequences against $LaPO_4$ and $TiO_2$ nanoparticles were discovered through peptide phage display technique as an application to biomolecular recognition of inorganic materials. Sequencing results showed that a motif consisting of serine and proline was commonly expressed in specific sequences. It was postulated that serine directly bound to nanoparticles using its terminal hydroxyl (OH) group. In this sense, oxygen atom seemed to work as a ligand to metal ions and hydrogen atom as a H-bond donor, was thought to bind to the oxygen atoms or the hydroxyl groups on particle surface. Also, it was expected that proline assists serine to make an ideal van der Waals contact between serine and nanoparticles, which optimizes the binding of peptide onto surface.

• Cartoon and Animation Studies
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• s.13
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• pp.237-253
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• 2008

Visual Effects have been revered as 'Spectacular' film elements for a long time, and once there was a misunderstanding that they destroyed the actual 'Story'. But, now they are becoming a valuable tool for storytellers. A film pursues a perfect narrative structure and visual reality so that the audience can believe the story as a real. Giving a narrative motif to the audience, they use Visual Effects that provide the technical solutions and -at the same time- they create and preserve the diegetic world that Is either believable or not. This research suggests that we analyze precisely and make a classified table of the narrative use of Visual Effects based on the previous research of Shilo T. McClean. First, we can ask if the narrative motif would be there in front of the camera, From there, we then can get two desired answers. One is, if there is nothing to visually stand up, Visual Effects can intervene as an alternative tool for creating the diegetic world. The other is that Visual Effects can be used for preserving the diegetic world as a necessary tool. Then, in the latter, we can consider whether there is a storyteller's purpose to be added, so we can distinguish the details. This classified Visual Effects for the narrative is able to dispense proof that they can be worthy as to provide a 'Spectacuiar' aura as to create and preserve the diegetic world. I would like to argue that this research could be a foundation for the inter-progress of future studies for visual effects as well as for their amazing technological improvements.

• Korean Journal of Poultry Science
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• v.38 no.2
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• pp.97-104
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• 2011

We conducted a 10-month (March to October 2009) surveillance of Newcastle disease virus (NDV) in 13 slaughterhouses in Korea. NDV was isolated in 13.0%, 13.3%, 16.0%, and 10.8% of chicken farms, transport vehicles, hang rooms, and chilling water, respectively. Of NDV isolates from slaughterhouses, 37% were isolated in July. All NDV isolates were determined to be lentogenic viruses by RT-PCR-based pathotyping, and all NDV isolates had the $^{112}GKQGR/L^{117}$ motif at the cleavage site of the F protein. Phylogenetic analysis based on the hypervariable region of the F protein gene classified all 25 NDV isolates examined into genotype I within class II. Of these, 24 were clustered together with the NDV V4 strain, while the remaining isolate was placed in the cluster belonging to the NDV Ulster 2C strain. Our results indicate that lentogenic NDV was a high-frequency contaminant in the serial process of ranging live birds to slaughtering at slaughterhouses.

• Journal of Microbiology and Biotechnology
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• v.31 no.2
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• pp.259-271
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• 2021

Many bacteria metabolize aromatic compounds via catechol as a catabolic intermediate, and possess multiple genes or clusters encoding catechol-cleavage enzymes. The presence of multiple isozyme-encoding genes is a widespread phenomenon that seems to give the carrying strains a selective advantage in the natural environment over those with only a single copy. In the naphthalene-degrading strain Pseudomonas putida ND6, catechol can be converted into intermediates of the tricarboxylic acid cycle via either the ortho- or meta-cleavage pathways. In this study, we demonstrated that the catechol ortho-cleavage pathway genes (catBICIAI and catBIICIIAII) on the chromosome play an important role. The catI and catII operons are co-transcribed, whereas catAI and catAII are under independent transcriptional regulation. We examined the binding of regulatory proteins to promoters. In the presence of cis-cis-muconate, a well-studied inducer of the cat gene cluster, CatRI and CatRII occupy an additional downstream site, designated as the activation binding site. Notably, CatRI binds to both the catI and catII promoters with high affinity, while CatRII binds weakly. This is likely caused by a T to G mutation in the G/T-N11-A motif. Specifically, we found that CatRI and CatRII regulate catBICIAI and catBIICIIAII in a cooperative manner, which provides new insights into naphthalene degradation.

• Korean Journal of Heritage: History & Science
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• v.51 no.1
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• pp.126-147
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• 2018

The compositions and iconographies of the three Illustrations of the Sixteen Contemplations produced in the early Joseon Dynasty effectively manifest the transitional period of Joseon society as well as the Joseon people's perception of the Pure Land. In particular, the painting at titled Chionji (知恩寺) dated 1435 and another painting at titled Chion' in (知恩院) from 1465, which were commissioned by the Joseon royal family and high-ranking monk, embody the Pure Land faith of the Tiantai School of Buddhism (天台宗) which thrived during the late Goryeo period. This indicates that the Joseon royal court continued to favor the Pure Land faith that emphasized salvation through "self-power" (自力), which was popular among both the royal family and the nobility of Goryeo. On the other hand, in the painting at titled $H{\bar{o}}rinji$ (法輪寺), which is presumed to have been made in the sixteenth century, the compositions and iconographies shown in late Goryeo examples of the Illustrations of the Sixteen Contemplations are disassembled. Moreover, a new iconographical motif, i.e. "welcoming the dragon boat" (龍船接引), emerged with this painting. This motif symbolizes the idea that the souls of the deceased are guided by Amitabha Buddha to rebirth in the Pure Land of Extreme Bliss, which is based on the "other-power" of the Pure Land faith that emphasizes the power of Amitabha Buddha in attaining salvation rather than the educational "self-power" of the Pure Land faith. The emergence of this motif demonstrates the transformation of the Pure Land belief into a faith that relied on the "other-power" of Amitabha in Joseon's Confucian society.

• Archives of design research
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• v.14 no.3
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• pp.177-186
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• 2001

Modern times is called the age of image. It means that our society's importance is transferring from the commodity-centered industrial society to intangible culture-oriented society Therefore, it is becoming very important that what kind of image, concept and psychological factor act upon the space, things, incident and time (event) which is constituted around our environment. As regards this standpoint, from the early period, that advanced countries have been taking advantage of the national symbol image very positive way and function for domestic things and place and event and so on which make a standout for the nation's positive image and taken an effort for promoting a pride of their fellow countrymen through this. This study approaches the basic images of national symbol which includes the country's name, national anthem, national flag through the design principle which could express some certain above level of pattern and composition. I suggested various applicative motif based on basic expressions of each individual image and the applied sample goods of this idea, and through the introduction of the process of image development, and I tried to offer a moment of more prosperity and development at a later time. This is for encouraging fellow citizens to use national symbol in the free and positive way which make them to increase a national pride, and give a familiar image in the citizens'daily life. I intended to offer basic materials for promoting ourselves whenever we need it. And also by the offering information on our nation for foreigners which make them to have a favorable impression of our nation. I tried to promote a positive national image.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2005.09a
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• pp.325-330
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• 2005

We are generally interested in the analysis, detection and prediction of structural motifs in proteins, in order to infer compatibility of amino acid sequence to structure in proteins of known three-dimensional structure available in the Protein Data Bank. In this context, we are analyzing some of the well-characterized structural motifs in proteins. We have analyzed simple structural motifs, such as, ${\beta}$-turns and ${\gamma}$-turns by evaluating the statistically significant type-dependent amino acid positional preferences in enlarged representative protein datasets and revised the amino acid preferences. In doing so, we identified a number of ‘unexpected’ isolated ${\beta}$-turns with a proline amino acid residue at the (i+2) position. We extended our study to the identification of multiple turns, continuous turns and to peptides that correspond to the combinations of individual ${\beta}$ and ${\gamma}$-turns in proteins and examined the hydrogen-bond interactions likely to stabilize these peptides. This led us to develop a database of structural motifs in proteins (DSMP) that would primarily allow us to make queries based on the various fields in the database for some well-characterized structural motifs, such as, helices, ${\beta}$-strands, turns, ${\beta}$-hairpins, ${\beta}$-${\alpha}$-${\beta}$, ${\psi}$-loops, ${\beta}$-sheets, disulphide bridges. We have recently implemented this information for all entries in the current PDB in a relational database called ODSMP using Oracle9i that is easy to update and maintain and added few additional structural motifs. We have also developed another relational database corresponding to amino acid sequences and their associated secondary structure for representative proteins in the PDB called PSSARD. This database allows flexible queries to be made on the compatibility of amino acid sequences in the PDB to ‘user-defined’ super-secondary structure conformation and vice-versa. Currently, we have extended this database to include nearly 23,000 protein crystal structures available in the PDB. Further, we have analyzed the ‘structural plasticity’ associated with the ${\beta}$-propeller structural motif We have developed a method to automatically detect ${\beta}$-propellers from the PDB codes. We evaluated the accuracy and consistency of predicting ${\beta}$ and ${\gamma}$-turns in proteins using the residue-coupled model. I will discuss results of our work and describe databases and software applications that have been developed.

• The Plant Pathology Journal
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• v.34 no.1
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• pp.11-22
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• 2018

Type VI secretion system (T6SS) has been discovered in a variety of gram-negative bacteria as a versatile weapon to stimulate the killing of eukaryotic cells or prokaryotic competitors. Type VI secretion effectors (T6SEs) are well known as key virulence factors for important pathogenic bacteria. In many Burkholderia species, T6SS has evolved as the most complicated secretion pathway with distinguished types to translocate diverse T6SEs, suggesting their essential roles in this genus. Here we attempted to detect and characterize T6SSs and potential T6SEs in target genomes of plant-associated and environmental Burkholderia species based on computational analyses. In total, 66 potential functional T6SS clusters were found in 30 target Burkholderia bacterial genomes, of which 33% possess three or four clusters. The core proteins in each cluster were specified and phylogenetic trees of three components (i.e., TssC, TssD, TssL) were constructed to elucidate the relationship among the identified T6SS clusters. Next, we identified 322 potential T6SEs in the target genomes based on homology searches and explored the important domains conserved in effector candidates. In addition, using the screening approach based on the profile hidden Markov model (pHMM) of T6SEs that possess markers for type VI effectors (MIX motif) (MIX T6SEs), 57 revealed proteins that were not included in training datasets were recognized as novel MIX T6SE candidates from the Burkholderia species. This approach could be useful to identify potential T6SEs from other bacterial genomes.

• Molecules and Cells
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• v.27 no.1
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• pp.47-54
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• 2009

A cDNA clone for a transcript preferentially expressed during an early phase of flooding was isolated from Nicotiana tabacum. Nucleotide sequencing of the cDNA clone identified an open reading frame that has high homology to the previously reported glycine-rich RNA-binding proteins. The open reading frame consists of 157 amino acids with an N-terminal RNA-recognition motif and a C-terminal glycine-rich domain, and thus the cDNA clone was designated as Nicotiana tabaccum glycine-rich RNA-binding protein-1 (NtGRP1). Expression of NtGRP1 was upregulated under flooding stress and also increased, but at much lower levels, under conditions of cold, drought, heat, high salt content, and abscisic acid treatment. RNA homopolymer-binding assay showed that NtGRP1 binds to all the RNA homopolymers tested with a higher affinity to poly r(G) and poly r(A) than to poly r(U) and poly r(C). Nucleic acid-binding assays showed that NtGRP1 binds to ssDNA, dsDNA, and mRNA. NtGRP1 suppressed expression of the fire luciferase gene in vitro, and the suppression of luciferase gene expression could be rescued by addition of oligonucleotides. Collectively, the data suggest NtGRP1 as a negative modulator of gene expression by binding to DNA or RNA in bulk that could be advantageous for plants in a stress condition like flooding.