• Proceedings of the Korean Society of Plant Pathology Conference
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• 2003.10a
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• pp.108.2-109
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• 2003

The Gyeonggi-do Agricultural Research and Extension Services has developed a web-site (www.epilove.com) in collaboration with EPINET to provide information on agricultural weather and rice disease and insect pest management in Gyeonggi-do. Weather information includes near real-time weather data monitored by automated weather stations (AWS) installed at rice paddy fields of 11 Agricultural Technology Centers (ATC) in Gyeonggi-do, and weekly weather forecast by Korea Meteorological Administration (KMA). Map images of hourly air temperature and rainfall are also generated at 309m x 309m resolution using hourly data obtained from AWS installed at 191 locations by KMA. Based on near real-time weather data from 11 ATC, hourly infection risks of rice blast, sheath blight, and bacterial grain rot for individual districts are estimated by disease forecasting models, BLAST, SHBLIGHT, and GRAINROT. Users can diagnose various diseases and insects of rice and find their information in detail by browsing thumbnail images of them. A database on agrochemicals is linked to the system for disease and insect diagnosis to help users search for appropriate agrochemicals to control diseases and insect pests.

• Journal of the Korea Institute of Information and Communication Engineering
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• v.20 no.9
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• pp.1816-1821
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• 2016

Protein secondary structure is important for the study of protein evolution, structure and function of proteins which play crucial roles in most of biological processes. This paper try to effectively extract protein secondary structure information from the large protein structure database in order to predict the protein secondary structure of a query protein sequence. To find more remote homologous sequences of a query sequence in the protein database, we used PSI-BLAST which can perform gapped iterative searches and use profiles consisting of homologous protein sequences of a query protein. The secondary structures of the homologous sequences are weighed combined to the secondary structure prediction according to their relative degree of similarity to the query sequence. When homologous sequences with a neural network predictor were used, the accuracies were higher than those of current state-of-art techniques, achieving a Q3 accuracy of 92.28% and a Q8 accuracy of 88.79%.

• Journal of Biomedical Engineering Research
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• v.25 no.6
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• pp.617-621
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• 2004

In recent, researchers in the field of Bioinformatics need to analyze thousands of genome sequences efficiently according to introduce of new analysis methods and technologies such as genome expression microchip. This rapid growth in the field of bio-engineering needs computing resources to analyze rapidly for genome sequences, but it does not introduce the computing resources due to an enormous investment expense. The core factor of this study is integrated environment based PC-Cluster system & high speed access rate up to 155Mbps, continuous collection system for bio-information at home and abroad. The results of the study are establishment & stabilization of information and communication infrastructure, establishment & stabilization of high performance computer network up to 155Mbps, development of PC-Cluster system with 32 nodes, a parallel BLAST on Cluster system, which can provides scalable speedup in terms of response time, and development of collection & search system for bio-information.

• Journal of Food Hygiene and Safety
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• v.34 no.5
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• pp.502-507
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• 2019

Cephalopods are one of the most important fishery resources in the world because of their desirable taste and nutritional value. In south Korea, one of the countries in which a large amount of seafood is consumed, cephalopods (e.g., octopus, squid, and cuttlefish) have an annual consumption rate of over 400,000 metric tons. In this study, octopus and squid products (n=28) sold on the market were monitored by analyzing sequences of DNA barcode markers (cytochrome c oxidase subunit I and 16S ribosomal RNA genes). For species identification, the NCBI BLAST database was screened with the sequences and analyzed as a query. In this BLAST search, twelve squid products showed 99-100% sequence identity to Dosidicus gigas (n=3) and Todarodes pacificus (n=9). In the case of the other 16 products that were declared using octopus as raw materials on the labels, six products were identified as Cistopus taiwanicus (n=1), Amphioctopus marginatus (n=1), Scaeurgus unicirrhus (n=1), and Dosidicus gigas (n=3). Monitoring results indicated that a significant percentage (37.5%) of mislabeling was present in octopus products sold on the South Korean market.

• Korean Journal of Agricultural Science
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• v.12 no.2
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• pp.206-241
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• 1985

Attempts to search infection period, infection speed in the tissue of neck blast of rice plant, location of inoculum source and effects of several conditions about the leaf sheath of rice plants for neck blast incidence have been made. 1. The most infectious period for neck blast incidence was the booting stage just before heading date, and most of necks have been infected during the booting stage and on heading date. But $Indica{\times}Japonica$ hybrid varieties had shown always high possibility for infection after booting stage. 2. Incubation period for neck blast of rice plants under natural conditions had rather a long period ranging from 10 to 22 days. Under artificial inoculation condition incubation period in the young panicle was shorter than in the old panicle. Panicles that emerged from the sheath of flag leaf had long incubation period, with a low infection rate and they also shown slow infection speed in the tissue. 3. Considering the incubation period of neck blast of rice plant, we assumed that the most effective application periods of chemicals are 5-10 days for immediate effective chemicals and 10-15 days for slow effective chemicals before heading. 4. Infiltration of conidia into the leaf sheath of rice plant carried out by saturation effect with water through the suture of the upper three leaves. The number of conidia observed in the leaf sheath during the booting stage were higher than those in the leaf sheath during other stages. Ligule had protected to infiltrate of conidia into the leaf sheath. 5. When conidia were infiltrated into the leaf sheath, the highest number of attached conidia was observed on the panicle base and panicle axis with hairs and degenerated panicle, which seemed to promote the infection of neck blast. 6. The lowest spore concentration for neck blast incidence was variable with rice varietal groups. $Indica{\times}Japonica$ hybrid varieties were infected easily compared to the Japonica type varieties, especially. The number of spores for neck blast incidence in $Indica{\times}Japonica$ hybrid varieties was less than 100 and disease index was higher also in $Indica{\times}Japonica$ hybrid than in Japonica type varieties. 7. Nitrogen content and silicate content were related with blast incidence in necks of rice plants in the different growing stage changed during growing period. Nitrogen content increased from booting stage to heading date and then decreased gradually as time passes. Silicate content increased from booting stage after heading with time. Change of these content promoted to increase neck blast infection. 8. Conidia moved to rice plant by ascending and desending dispersal and then attached on the rice plant. Conidia transfered horizontally was found very negligible. So we presumed that infection rate of neck blast was very low after emergence of panicle base from the leaf sheath. Also ascending air current by temperature difference between upper and lower side of rice plant seemed to increase the liberation of spores. 9. Conidial number of the blast fungus collected just before and after heading date was closely related with neck blast incidence. Lesions on three leaves from the top were closely related with neck blast incidence, because they had high potential for conidia formation of rice blast fungus and they were direct inoculum sources for neck blast. 10. The condition inside the leaf sheath was very favorable for the incidence of neck blast and the neck blast incidence in the leaf sheath increased as the level of fertilizer applied increased. Therefore, the infection rate of neck blast on the all panicle parts such as panicle base, panicle branches, spikelets, nodes, and internodes inside the leaf sheath didn't show differences due to varietal resistance or fertilizers applied. 11. Except for others among dominant species of fungi in the leaf sheath, only Gerlachia oryzae appeared to promote incidence of neck blast. It was assumed that days for heading of varieties were related with neck blast incidence.

• Korean Journal of Poultry Science
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• v.34 no.2
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• pp.85-90
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• 2007

The chicken liver has been involved in various biological functions including detoxification, glycogen storage and plasma protein synthesis. The aim of this study was to investigate differentially expressed genes in chicken liver in four different growing stages. Using 10 arbitrary Annealing Control Primers (ACPs), five differentially expressed genes have been identified. Based on the Basic Local Alignment Search Tool (BLAST) search results, three of them were matched with previously known genes, and the other two were matched with unknown EST sequence and a hypothetical protein, respectively. In order to confirm the expression results, quantitative real-time PCR was also performed. The high similarities between the expression data using arbitrary ACPs and quantitative real-time PCR indicate that the identified genes are the real differentially expressed genes in different growing stages. The genes identified in this study can be used as valuable biomarkers in chicken with further investigation of the functions.

• Journal of Plant Biotechnology
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• v.29 no.3
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• pp.161-170
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• 2002

For the hairy root of Panax ginseng, we have got mass spectrums from MALDI/TOF/MS analysis and Tandem mass spectrums from ESI/Q-TOF/MS analysis. While mass spectrum provides the molecular weights of peptide fragments digested by protease such as trypsin, tandem mass spectrum produces amino acid sequence of digested peptides. Each amino acid sequences can be a query sequence in BLAST search to identify proteins. For the specimens of animals or plants of which genome sequences were known, we can easily identify expressed proteins from mass spectrums with high accuracy. However, for the other specimens such as ginseng, it is difficult to identify proteins with accuracy since all the protein sequences are not available yet. Here we compared the mass spectrums and the peptide amino acid sequences with ginseng expressed sequence tag (EST) DB. The matched EST sequence was used as a query in BLAST search for protein identification. They could offer the correct protein information by the sequence alignment with EST sequences. 90% of peptide sequences of ESI/Q-TOF/MS are matched with EST sequences. Comparing 68% matches of the same sequences with the nr database of NCBI, we got more matches by 22% from ginseng EST sequence search. In case of peptide mass fingerprinting from MALDI/TOF/MS, only about 19% (9 proteins of 47 spots) among peptide matches from nr DB were correlated with ginseng EST DB. From these results, we suggest that amino acid sequencing using tandem mass spectrum analysis may be necessary for protein identification in ginseng proteome analysis.

• Environmental Mutagens and Carcinogens
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• v.24 no.2
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• pp.85-90
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• 2004

Nickel(II) compounds are carcinogenic metals which induce genotoxicity and oxidative stress through the generation of reactive oxygen species. In search of new molecular pathways toward understanding the molecular mechanism of nickel(II)-induced carcinogensis, we performed mRNA differential display analysis using total RNA extracted from nickel(II) acetate-treated normal rat kidney cells (NRK-52E). Cells were exposed for 3 days to 160 and 240 uM nickel(II) concentrations. cDNAs corresponding to mRNAs for which expression levels were altered by nickel(II) were isolated, sequenced, and followed by a GenBank Blast homology search. Specificity of differential expression of cDNAs was determined by RT-PCR and Western blot analysis. Two of them (SH3BGRL3 and FHIT) were down-regulated and one (metallothionein) was up-regulated by nickel(II) treatment. The expression of these mRNAs were nickel(II) concentration-dependent. The levels of FHIT and metallothionein proteins were also consistent with the results for mRNAs. Overall, although the fundamental questions related to function of these genes in nickel(II)-mediated carcinogenicity are not answered, our study suggests that they can be interesting candidates for studies of molecular mechanisms of nickel(II) carcinogenesis.

• International journal of advanced smart convergence
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• v.8 no.1
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• pp.1-8
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• 2019

Coronaviruses are known respiratory pathogens. In the past, most human coronaviruses were thought to cause mild symptoms such as cold. However recently, as seen in the Severe Acute Respiratory Syndrome (SARS) and the Middle East Respiratory Syndrome (MERS), infectious diseases with severe pulmonary disease and respiratory symptoms are caused by coronaviruses, making research on coronaviruses become important. Considering previous studies, we constructed 'HCoV-IMDB (Human Corona Virus Immune Database)' to systematically provide genetic information on human coronavirus and host immune information, which can be used to analyze the interaction between human coronavirus and host immune proteins. The 'HCoV-IMDB' constructed in the study can be used to search for genetic information on human coronavirus and host immune protein and to download data. A BLAST search specific to the human coronavirus, one of the database functions, can be used to infer genetic information and evolutionary relationship about the query sequence.

• Bulletin of the Korean Chemical Society
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• v.32 no.11
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• pp.4016-4020
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• 2011

A number of mimetic peptides of apolipoprotein A-I, a major component for high density lipoproteins (HDL), were screened from the phase-displayed random peptide library by utilizing monoclonal antibodies (A12). A mimetic peptide for A12 epitope against apolipoprotein A-I was selected as FVLVRDTFPSSVCCP(pA2) exhibiting 45% homology with Apo A-I in the BLAST search. Solution structure determination of this mimotope was made by using 2D-NMR data and NMR-based distance geometry (DG)/molecular dynamic calculations. The resulting DG structures had low penalty value of 0.4-0.6 ${\AA}^2$ and the total RMSD of 0.7-1.7 ${\AA}$. The mimotope pA2 exhibited a characteristic ${\beta}$-turn conformation from Val[2] to Phe[8] near Pro[9] residue.