• The Korea Journal of Herbology
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• v.34 no.5
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• pp.1-12
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• 2019

Objectives : The consumption of licorice is large in Korea, but domestic production is insufficient due to the lack of adaptability. This study aimed to provide a morphological basis for adding interspecific hybrid licorice with improved adaptability to pharmacopoeia. Methods : This study was to establish identification criteria for the original plants, external and internal morphology of the authentic herbal medicines (Glycyrrhiza uralensis, G. glabra and G. inflata), market products and artificially interspecific hybrid forms of licorice. For this purpose, previous studies were investigated and visual and histological observations were carried out. We focused on the internal morphology by microscopic observation for securing objectivity. Finally, we proposed the identification keys for precise classification of each part. Results : 1) Original plant : Licorice species in the compendium were distinguished by the number of leaflets, presence of hair on the fruit, curvature and swelling of the fruit. 2) External morphology : Licorice species were distinguished by degree of powderiness, tearing gap, radial structure in the cross section and existence of protrusion of outer epidermis. 3) Internal morphology : Licorice species were distinguished by the degree of development of phloem fiber bundle, development of obliterated sieve, whether the secondary medullary ray are branched. In the case of interspecific hybrids, the characteristics of both species used for hybridization were mixed in all observation methods. Conclusions : These results suggest that the interspecific crossbred licorice is suitable for the pharmacopoeial standard. Therefore, it can be applied as a herbal medicine through additional supplementary study.

• 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.

• Korean Journal of Ecology and Environment
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• v.44 no.1
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• pp.95-101
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• 2011

Present study aimed to investigate morphological change and gene expression in the gill of Cyprinus carpio after exposure against muddy water caused by riverbed disturbance with various rearing condition. The gill of C. carpio showed abnormal shapes in its secondary lamellae and a rough surface with impure debris after exposed to muddy water for 80 days. In addition, the gills showed the edema, the exfoliation of epithelial cell, and the fusion of the secondary lamellae. Using 20 ACPs, 24 differentially expressed genes (DEGs) exposed to muddy water for 80 days were identified. 17 genes among them were up-regulated, while 7 genes were down-regulated in preterm deliveries. A BLAST searches revealed that 3 genes were revealed known genes as calcium transporter 1 (TRPV6) mRNA, macha mRNA for putative puroindoline b protein, and Efnb3 protein-like. Therefore, it is considered that Efnb3 gene from gill would be a useful indicator for neurobehavioral changes in fish influenced by muddy water.

• Asian Pacific Journal of Cancer Prevention
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• v.14 no.7
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• pp.4167-4175
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• 2013

A najor current challenge and constraint in cervical cancer research is the development of vaccines against human papilloma virus (HPV) epitopes. Although many studies are done on epitope identification on HPVs, no computational work has been carried out for high risk forms which are considered to cause cervical cancer. Of all the high risk HPVs, HPV 16, HPV 18 and HPV 45 are responsible for 94% of cervical cancers in women worldwide. In this work, we computationally predicted the promiscuous epitopes among the E6 proteins of high risk HPVs. We identified the conserved residues, HLA class I, HLA class II and B-cell epitopes along with their corresponding secondary structure conformations. We used extremely precise bioinformatics tools like ClustalW2, MAPPP, NetMHC, Epi,Jen, EpiTop 1.0, ABCpred, BCpred and PSIPred for achieving this task. Our study identified specific regions 'FAFR(K)DL' followed by 'KLPD(Q)LCTEL' fragments which proved to be promiscuous epitopes present in both human leukocyte antigen (HLA) class I, class II molecules and B cells as well. These fragments also follow every suitable character to be considered as promiscuous epitopes with supporting evidences of previously reported experimental results. Thus, we conclude that these regions should be considered as the important for design of specific therapeutic vaccines for cervical cancer.

• Journal of Microbiology
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• v.45 no.3
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• pp.262-267
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• 2007

During a screening program, an actinomycete strain isolated from the Egyptian soil was investigated for its potential to show antimicrobial activity. The identification of this isolate was performed according to spore morphology and cell wall chemo-type, which suggested that this strain is a streptomycete. Further cultural, physiological characteristics and the analysis of the nucleotide sequence of the 16S rRNA gene (1480 bp) of this isolate indicated that this strain is identical to Streptomyces violaceusniger (accession number EF063682) and then designated S. violaceusniger strain HAL64. In its culture supernatant, this organism could produce one major compound strongly inhibits the growth of Gram-positive but the inhibition of Gram-negative indicator bacteria was lower. The antibiotic was separated by silica gel column chromatography and then purified on a sephadex LH-20 column and finally the purity was checked by HPLC. The chemical structure of the purified compound was determined using spectroscopic analyses (molecular formula of $C_{33}H_{32}N_{2}O_{10}$ and molecular weight of 617.21) and found to be identical to the kosinostatin, a quinocycline antibiotic which is known to be produced by Micromonspora sp. TP-A0468 (Igarashi et al., 2002) and to quinocycline B isolated from Streptomyces aureofaciens (Celmer et al., 1958). Although the antibiotic is known, the newly isolated strain was able to produce the antibiotic as a major product providing an important biotechnological downstream advantage.

• Journal of Bio-Environment Control
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• v.23 no.2
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• pp.123-130
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• 2014

Oriental melon (Cucumis melo var. makuwa) should be cultivated on the soil and be harvested. It is difficult to find because it is covered with leaves, and furthermore, it is very hard to grip it due to its climbing stems. This study developed and tested oriental melon harvesting robots such as an end-effector, manipulator and identification device. The end effector is divided into a gripper for harvest and a cutter for stems. In addition, it was designed to control the gripping and cutting forces so that the gripper could move four fingers at the same time and the cutter could move back and forth. The manipulator was designed to realize a 4-axis manipulator structure to combine orthogonal coordinate-type and shuttle-type manipulators with L-R type model to rotate based on the central axis. With regard to the identification device, oriental melon was identified using the primary identification global view camera device and secondary identification local view camera device and selected in the prediction of the sugar content or maturity. As a result of the performance test using this device, the average harvest time was 18.2 sec/ea, average pick-up rate was 91.4%, average damage rate was 8.2% and average sorting rate was 72.6%.

• Geophysics and Geophysical Exploration
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• v.7 no.2
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• pp.121-129
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• 2004

The geostatistical approach was applied to integrate MT (Magneto-telluric) resistivity data and borehole information for the spatial RMR (Rock Mass Rating) evaluation. Generally, resistivity of the subsurface is believed to be positively related to the RMR, thus the resistivity and borehole RMR information was combined in a geostatistical approach. To relate the two different sets of data, we take the MT resistivity data as secondary information and estimate the RMR mean values at unsampled points by identification of the resistivity to the borehole data. Two types of approach are performed for the estimation of RMR mean values. Then the residuals of the RMR values around the borehole sites are geostatistically modeled to infer the spatial structure of difference between real RMR values and estimated mean values. Finally, this geostatistical estimation is added to the previous means. The result applied to a real situation shows prominent improvements to reflect the subsurface structure and spatial resolution of RMR information.

• Journal of Life Science
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• v.7 no.3
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• pp.161-166
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• 1997

HIV-1 Rev protein plays an important role in regulating the expression of viral structural proteins. It allows the nuclear export and accumulation of unspliced and partially spliced viral mRNA in the cytoplasm. The Rev-responsive element RNA, present in the env gene, forms a higly ordered RNA secondary structure and is required for the Rev-mediated mRNA export. For this process to complete factor(s) are strongly suggested. From our experiments of electrophoretic mobility shift, UV-crosslinking and SDS/PAGE, RRE RNA was found to be recognized to several nuclear factors such as 36/37, 56, 41. 76, 150 kD proteins in the order of reactivity. Among them, 36/37 and 56 kD proteins are more reactive upon a brief UV treatment (5 min) and more persistent in the presence of high amount of nonspecific competitor, heparin. Certain nuclear protein9s) seemed to recognize the RRE RNA structure in competition with Rev to gel mobility shift assay.

• International Journal of Industrial Entomology and Biomaterials
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• v.31 no.1
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• pp.14-19
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• 2015

In a previous report, we identified several candidate antimicrobial peptides through de novo RNA sequencing of the centipede Scolopendra subspinipes mutilans. Here, we identify and characterize one of these peptides, Scolopendrasin I. We identified the centipede antimicrobial peptide Cecropin from the centipede transcriptome using an SVM algorithm, and subsequently analyzed the amino acid sequence for predicted secondary structure using a GOR algorithm. We identified an alpha helical region of Cecropin and named it Scolopendrasin I. We then assessed antimicrobial and hemolytic activity of Scolopendrasin I. Scolopendrasin I showed antimicrobial activity against various microbes, including antibiotic-resistant Gram-negative bacteria, in a radial diffusion assay. Scolopendrasin I had potent antibacterial activity against acne-associated microbes in a colony count assay and showed no hemolytic activity in a hemolysis assay. In addition, we confirmed that Scolopendrasin I bound to the surface of bacteria via a specific interaction with lipoteichoic acid and lipopolysaccharide, two components of bacterial cell membranes. In conclusion, the results presented here provide evidence that this is an efficient strategy for antimicrobial peptide candidate identification and that Scolopendrasin I has potential for successful antibiotic development.

• The Journal of the Acoustical Society of Korea
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• v.11 no.2
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• pp.59-67
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• 1992

Recently, the problem which actively control the unwanted noise propagated from the technical structure by the generated secondary sound has become considerable topic from the environmental preservation point of view. In most of these studies, active noise control deals with a plane wave propagation at low frequency using adaptive filtering techniques. On the other hand, in real acoustic systems are mostly short due to the limitation of geometric configuration. In this case, the acoustic properties such as reflections and resonances inside the acoustic system should be considered. In this paper, the acoustic modeling method for short length duct was introduced using the transfer matrix method, and the active noise control problem was investigated with \implementation of FIR filter for the transfer function of control system derived from this modeling method. The identification methods for the acoustic model of actual control system was proposed by numerical computation technique based on the estimation of optimal FIR filter coefficients. The acceptable attenuation on the real acoustic system and stability of the controller are predicted in this computational simulation.