• Proceedings of the Korean Society of Life Science Conference
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• 2002.12a
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• pp.20-47
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• 2002

Two-dimensional gel electrophoresis (2-DE) maps for human stomach tissue proteins have been prepared by displaying the protein components of the tissue by 2-DE and identifying them using mass spectrometry. This will enable us to present an overview of the proteins expressed In human stomach tissues and lays the basis for subsequent comparative proteome analysis studies with gastric diseases such as gastric cancer. In this study, 2-DE maps of soluble fraction proteins were prepared on two gel images with partially overlapping pH ranges of 4-7 and 6-9. On the gels covering pH 4-7 and pH 6-9, about 900 and 600 protein spots were detected on silver staining, respectively. For protein identification, proteins spots on micropreparative gels stained by colloidal Coomassie Brilliant Blue G-250 were excised, digested in-gel with trypsln, and analyzed by peptide mass fingerprinting with delayed extraction-matrix assisted laser dosorption/ionization-mass spectrometry (DE-MALDI-MS). In all, 243 protein spots (168 spots in acidic map and 75 spots in basic map) corresponding to 136 different proteins were identified. Besides these principal maps, maps of lower resolution, i.e. overview maps (displayed on pH 3-10 gels) for total homogenate and soluble fraction, are also presented with some identifications mapped on them. Based on the 2-DE maps presented in this study, a 2-DE database for human stomach tissue proteome has been constructed and available at http://proteome.gsnu.ac.kr/DB/2DPAGE/Stomach/. The 2-DE maps and the database resulting from this study will serve important resources for subsequent proteomic studies for analyzing the normal protein variability in healthy tissues and specific protein variations in diseased tissues.

• Asian Pacific Journal of Cancer Prevention
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• v.17 no.8
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• pp.4003-4007
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• 2016

Long interspersed elements-1s (LINE-1s) are dispersed all over the human genome. There is evidence that hypomethylation of LINE-1s and levels of sex steroids regulate gene expression leading to cancer development. Here, we compared mRNA levels of genes containing an intragenic LINE-1 in breast cancer cells treated with various sex steroids from Gene Expression Omnibus (GEO), with the gene expression database using chi-square analysis (http://www.ncbi.nlm.nih.gov/geo). We evaluated whether sex steroids influence expression of genes containing an intragenic LINE-1. Three sex steroids at various concentrations, 1 and 10 nM estradiol (E2), 10 nM progesterone (PG) and 10 nM androgen (AN), were assessed. In breast cancer cells treated with 1 or 10 nM E2, a significant percentage of genes containing an intragenic LINE-1 were down-regulated. A highly significant percentage of E2-regulated genes containing an intragenic LINE-1 was down-regulated in cells treated with 1 nM E2 for 3 hours (p<3.70E-25; OR=1.91; 95% CI=2.16-1.69). Similarly, high percentages of PG or AN-regulated genes containing an intragenic LINE-1 wwere also down-regulated in cells treated with 10 nM PG or 10 nM AN for 16 hr (p=9.53E-06; OR=1.65; 95% CI=2.06-1.32 and p=3.81E-14; OR=2.01; 95% CI=2.42-1.67). Interestingly, a significant percentage of AN-regulated genes containing an intragenic LINE-1 was up-regulated in cells treated with 10 nM AN for 16 hr (p=4.03E-02; OR=1.40; 95% CI=1.95-1.01). These findings suggest that intragenic LINE-1s may play roles in sex steroid mediated gene expression in breast cancer cells, which could have significant implications for the development and progression of sex steroid-dependent cancers.

• Korean Journal of Soil Science and Fertilizer
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• v.48 no.6
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• pp.588-592
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• 2015

Soil testing is one of the major strategies for establishing sustainable agricultural practice as it analyzes nutrient contents of soil and determines the amount of nutrients required for crop growth. Soil testing for the field cultivating regional major crops in Korea has been conducting by National Academy of Agricultural Science (NAAS), provincial agricultural research & extension services and agriculture technology centers since 2000. 1,006,227 soil samples were analyzed and uploaded on Korean soil information system (http://soil.rda.go.kr) from 2003 to 2013. Soil pH has changed from 6.1 to 6.2. Organic matter (OM), available (Avail.) phosphate and exchangeable (Exch.) K have decreased from 24 to $23gkg^{-1}$, 541 to $399mgkg^{-1}$ and 0.90 to $0.72cmol_ckg^{-1}$ between 2003 and 2013, respectively. Especially, Exch. Ca contents decreased to $5.7cmol_ckg^{-1}$ in 2009 and increased to $6.2cmol_ckg^{-1}$ in 2013. Ratios of optimal ranges for cropping were 48% for pH, 22% for OM, 26% for Avail. phosphate, and 23, 16, 22% for Exch. K, Ca and Mg in 2013. Ratios of optimal ranges for pH increased and low ranges for OM, Avail. phosphate and Exch. K increased. Frequency distribution was 64% for pH 5.5~7.0, 65% for OM $10{\sim}30gkg^{-1}$, 48% for Avail. phosphate under $300mgkg^{-1}$ and 23, 29, 22% for Exch. K 0.2~0.6, Ca 4.0~6.0 and Mg $1.0{\sim}1.5cmol_ckg^{-1}$.

• Journal of KIISE:Software and Applications
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• v.36 no.10
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• pp.851-860
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• 2009

Recently, among the computational methods of protein-protein interaction prediction, vast amounts of domain based methods originated from domain-domain relation consideration have been developed. However, it is true that multi domains collaboration is avowedly ignored because of computational complexity. In this paper, we implemented a protein interaction prediction system based the Interaction Significance matrix, which quantified an influence of domain combination pair on a protein interaction. Unlike conventional domain combination methods, IS matrix contains weighted domain combinations and domain combination pair power, which mean possibilities of domain collaboration and being the main body on a protein interaction. About 63% of sensitivity and 94% of specificity were measured when we use interaction data from DIP, IntAct and Pfam-A as a domain database. In addition, prediction accuracy gradually increased by growth of learning set size, The prediction software and learning data are currently available on the web site.

• Asian Pacific Journal of Cancer Prevention
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• v.15 no.8
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• pp.3767-3772
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• 2014

Introduction: MicroRNAs have emerged as post-transcriptional regulators that are critically involved in tumorigenesis. This study was designed to explore the effect of miRNA 133b on the proliferation and expression of TBPL1 in colon cancer cells. Methods: Human colon cancer SW-620 cells and human colon adenocarcinoma HT-29 cells were cultured. MiRNA 133b mimcs, miRNA 133b inhibitors, siRNA for TBPL1 and scrambled control were synthesized and transfected into cells. MiR-133b levels in cells and CRC tumor tissue was measured by real-time PCR. TBPL1 mRNA was detected by RT-PCR. Cell proliferation was studied with MTT assay. Western blotting was applied to detect TBPL1 protein levels. Luciferase assays were conducted using a pGL3-promoter vector cloned with full length of 3'UTR of human TBPL1 or 3'UTR with mutant sequence of miR-133b target site in order to confirm if the putative binding site is responsible for the negative regulation of TBPL1 by miR-133b. Results: Real time PCR results showed that miRNA 133b was lower in CRC tissue than that in adjacent tissue. After miR-133b transfection, its level was elevated till 48h, accompanied by lower proliferation in both SW-620 and HT-29 cells. According to that listed in http://www.targetscan.org, the 3'-UTR of TBPL1 mRNA (NM_004865) contains one putative binding site of miR-133b. This site was confirmed to be responsible for the negative regulation by miR-133b with luciferase assay. Further, Western blotting and immunohistochemistry both indicated a higher TBPL1 protein expression level in CRC tissue. Finally, a siRNA for TBPL1 transfection obviously slowed down the cell proliferation in both SW-620 and HT-29 cells. Conclusion: MiR-133b might act as a tumor suppressor and negatively regulate TBPL1 in CRC.

• Proceedings of the Korean Institute of Information and Commucation Sciences Conference
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• 2008.10a
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• pp.340-347
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• 2008

Ubiquitous services are high quality and differentiated services which are provided for users by recognizing the context of users and environmental conditions actively. In this case, context-aware middleware is one of the most important technologies required to implement the ubiquitous services. In this paper, we propose a method for providing ubiquitous services in a specific user space effectively and monitoring human bio-sensors. That is, the design and implementation of intelligent home service middleware and monitoring bio-sensors based on context awareness is discussed here. Context information from various sensors is gathered, and suitable services are inferred and provided to users by the middleware system. In our approach, user services can be modelled easily by using facts and rules, and the system can be extended easily to support various ubiquitous services other than intelligent home services also. The system can be integrated with external applications and legacy systems effectively by using various protocols such as RMI, socket and HTTP, XML and etc. We have designed and evaluated various facts and rules for intelligent home services in real environments. Functionality evaluation with the system shows that ubiquitous services can be provided to users effectively in a home environment.

• Biomolecules & Therapeutics
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• v.16 no.4
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• pp.431-436
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• 2008

To identify genes whose expression correlated with biological features of therapy-related AML (t-AML), we analyzed the expression profiles of de novo AML t(9;11) and t-AML t(9;11) bone marrow samples using previously published SAGE data. Three-hundred twenty-nine transcripts that satisfied statistical (P<0.05) and magnitude-of-change ($\geq$ 4-fold) criteria were identified as differentially expressed between de novo AML t(9;11) and t-AML t(9;11) cells. Of these transcripts, 301 (91%) matched known genes or ESTs and were classified according to functional categories (http://david.abcc.ncifcrf.gov/). The majority of differentially expressed genes in t-AML t(9;11) were involved in the regulation of biological and metabolic processes. Especially prominent among these were genes related to immune and drug responses. These results establish a framework for developing new drugs for the treatment of t-AML.

• Korean Journal of Health Education and Promotion
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• v.24 no.2
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• pp.15-28
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• 2007

Objectives: In this paper, the survey on internet usage patterns of health consumers was conducted and analyzed in order to determine internet health information assessment criteria for providing correct consumer health information on web-sites. Methods: By using a survey questionnaire with 16 questions on general information and 20 questions on internet health information, data were collected from September 16 to 25, 2005 from 476 participants through an internet web site, http://www.hp.go.kr. Frequency analysis, t-test, and multiple regression were used in order to analyze the difference in assessment criteria, factors influencing assessment criteria, factors influencing user satisfaction, etc. Results: General characteristics of the study population were: the persons over age 40 were the smallest age group; women were accounted for 74.2%; and the persons with average income were the largest income group; and the persons with average health status were the largest health group. Most widely used health information were: exercise, disease, and diet, in order. There was significant difference(p=.001) in importance of assessment criteria between the persons in medical institutions and the persons not in medical institutions. There was no significant difference in other assessment criteria. We also found that contents of websites and easy to use were more important factors than elucidation of information providers and information sources including speciality of information in quality assessment criteria of internet health information. Discussion and Conclusion: Results of this paper were compared with the previous studies from the literatures. Contrary to the previous studies in the literature, there was significant difference in importance of assessment criteria between the persons in medical institutions and the persons not in medical institutions. In order to apply the study results to develop health contents for consumer, there is a need for further upgrade the proposed assessment criteria based on expert opinion.

• Genomics & Informatics
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• v.3 no.3
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• pp.86-93
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• 2005

Human brain EST data provide important clues for our understanding of the molecular biology associated with the function of the normal brain and the molecular pathophysiology with brain disorders. To systematically and efficiently study the function and disorders of the human brain, 45,773 human brain ESTs were collected from 27 human brain cDNA libraries, which were constructed from normal brains and brain disorders such as brain tumors, Parkinson's disease (PO) and epilepsy. An analysis of 45,773 human brain ESTs using our EST analysis pipeline resulted in 38,396 high-quality ESTs and 35,906 ESTs, which were coalesced into 8,246 unique gene clusters, showing a significant similarity to known genes in the human RefSeq, human mRNAs and UniGene database. In addition, among 8,246 gene clusters, 4,287 genes ($52\%$) were found to contain full-length cONA clones. To facilitate the extraction of useful information in collected these human brain ESTs, we developed a user-friendly interface system, the Korea Brain Unigene Database (KBUD). The KBUD web interface allows access to our human brain data through three major search modes, the BioCarta pathway, keywords and BLAST searches. Each result when viewed in KBUD offers comprehensive information concerning the analyzed human brain ESTs provided by our data as well as data linked to various other publiC databases. The user-friendly developed KBUD, the first world-wide web interface for human brain EST data with ESTs of human brain disorders as well as normal brains, will be a helpful system for developing a better understanding of the underlying mechanisms of the normal brain well as brain disorders. The KBUD system is freely accessible at http://kugi.kribb.re.kr/KU/cgi -bin/brain. pI.

• Korean Journal of Environmental Agriculture
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• v.40 no.4
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• pp.279-289
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• 2021

BACKGROUND: Recently, the golden apple snail, Pomacea canaliculata has been used as an environmentally-friendly weed-control agent in rice farming. Although effective for this particular style of farming, P. canaliculata can be destructive to other crops. The objective of this study was to identify overwintering as well as regional and seasonal distribution characteristics of P. canaliculata. Notably, winter is typically fatal for P. canaliculata. However, owing to increasing average global temperatures, we assessed the ability of P. canaliculata to survive through uncharacteristically warm winters. METHODS AND RESULTS: To examine the distribution and overwintering regions of P. canaliculata, We conducted a survey from April 2020 to May 2021 on environmentally-friendly rice fields, agricultural waterways, and streams in 23 cities belonging to 8 provinces. In addition, because air temperature may influence the distribution density of P. canaliculata, we analyzed the winter temperature data (http://weather.rda.go.kr). CONCLUSION(S): In 2021, overwintering of P. canaliculata (1-3 individuals/m²) was observed in the Goheung and Yeongam regions in Jeonnam. Overwintering of P. canaliculata was observed in fewer regions in 2021 than in 2020; this fact may be attributed to the lower minimum temperatures measured in 2021 (approximately 8℃ lower) than those in 2020. Our results suggest that overwintering occurs as long as overnight temperatures are ≥ -15℃, but can take place if temperatures are as low as -19℃.