• Proceedings of the Korean Society for Bioinformatics Conference
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• 2003.10a
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• pp.26-51
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• 2003

Large scale protein interaction maps provide a new, global perspective with which to analyse protein function. PSIMAP, the Protein Structural Interactome Map, is a database of all the structurally observed interactions between superfamilies of protein domains with known three-dimensional structure in thePDB. PSIMAP incorporates both functional and evolutionary information into a single network. It makes it possible to age protein domains in terms of taxonomic diversity, interaction and function. One consequence of it is to predict the most important protein domain structure in evolution. We present a global analysis of PSIMAP using several distinct network measures relating to centrality, interactivity, fault-tolerance, and taxonomic diversity. We found the following results: ${\bullet}$ Centrality: we show that the center and barycenter of PSIMAP do not coincide, and that the superfamilies forming the barycenter relate to very general functions, while those constituting the center relate to enzymatic activity. ${\bullet}$ Interactivity: we identify the P-loop and immunoglobulin superfamilies as the most highly interactive. We successfully use connectivity and cluster index, which characterise the connectivity of a superfamily's neighbourhood, to discover superfamilies of complex I and II. This is particularly significant as the structure of complex I is not yet solved. ${\bullet}$ Taxonomic diversity: we found that highly interactive superfamilies are in general taxonomically very diverse and are thus amongst the oldest. This led to the prediction of the oldest and most important protein domain in evolution of lift. ${\bullet}$ Fault-tolerance: we found that the network is very robust as for the majority of superfamilies removal from the network will not break up the network. Overall, we can single out the P-loop containing nucleotide triphosphate hydrolases superfamily as it is the most highly connected and has the highest taxonomic diversity. In addition, this superfamily has the highest interaction rank, is the barycenter of the network (it has the shortest average path to every other superfamily in the network), and is an articulation vertex, whose removal will disconnect the network. More generally, we conclude that the graph-theoretic and taxonomic analysis of PSIMAP is an important step towards the understanding of protein function and could be an important tool for tracing the evolution of life at the molecular level.

• Asian Pacific Journal of Cancer Prevention
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• v.15 no.6
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• pp.2517-2522
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• 2014

Background: Several recent studies have explored associations between pre-mir-218 polymorphism (rs11134527) and cancer risk. However, published data are still inconclusive. To obtain a more precise estimation of the relationship in the Chinese population, we carried out a meta-analysis for the first time. Materials and Methods: Through retrieval from the PubMed, Medline, Embase, Web of Science databases, China National Knowledge Infrastructure and the Chinese BioMedical Literature Database, a total of four studies were analyzed with 3,561 cases and 3,628 controls for SNP pre-mir-218 rs11134527. We calculated odds ratios (ORs) and 95% confidence intervals (95%CIs) to explore the strength of associations. Results: The results showed that the rs11134527 polymorphism was associated with decreased cancer risk in GG versus AA and GG versus AA+AG models tested ( GG vs AA: OR=0.82, 95%CI: 0.71-0.94; GG vs AA+AG: OR=0.84, 95%CI: 0.74-0.96), and significantly decreased cervical cancer risk was observed in GG versus AA and GG versus AA+AG models (GG vs AA: OR=0.79, 95%CI: 0.66-0.94; GG vs AA+AG: OR=0.80, 95%CI: 0.68-0.94). However, no significant association between the rs11134527polymorphism and hepatocellular carcinoma risk was observed in all comparison models tested (AG vs AA: OR=0.94, 95%CI: 0.79-1.11; GG vs AA: OR=0.88, 95%CI: 0.70-1.10; GG+AG vs AA: OR=0.92, 95%CI: 0.79-1.08; GG vs AA+AG: OR=0.91, 95%CI: 0.75-1.11). Conclusion: The findings suggest that pre-miR-218 rs11134527 polymorphism may have some relation to cancer development in Chinese. However, well-designed studies with larger sample size and more detailed data are needed to confirm these conclusions.

• Journal of the Korean Institute of Landscape Architecture
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• v.42 no.3
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• pp.35-49
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• 2014

In this study, the faunae before and after creating the Solbangjuk Wetland Ecological Park located in Jecheon-city were compared. As a result, the change of the fauna according to the creation of the park showed the phenomenon that the species having the strong wilderness are reduced and the rate of general species become higher. In addition, the species which receive the restrictions for moving such as mammals, amphibians and reptiles are being gradually decreased by the increased visitors owing to the creation of the park. Moreover because there was the case where group of fishes have died caused by discharging and working the water in the reservoir during the creation process of the park, the supplementation work for this is required. However, it showed that the insects sucking the honey from flowers in the composed flower garden after creating the park, and the aquatic insects which live in this park that the stable water system for the growth of wetland plants is maintained, are increased, respectively. As a result of this survey, because the reservoir for agriculture adjacent to the residential area is generally small, the securing of the habitat space for the wild animals living in this park when creating the ecological parks seems to be necessary. The countermeasure should be considered so that some areas of the reservoir can be maintained in their natural state by adjusting the visitors' trails and the position of facilities for in order to secure the habitat of the wild animals.

• Research in Plant Disease
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• v.12 no.3
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• pp.254-259
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• 2006

Bacillus spp. isolated from mushroom medium wastes were evaluated for their biocontrol potentials on control of Sclerotinia rot of lettuce. The Bacillus isolates were more effectively obtained from waste suspension when directly added into nutrient agar(NA) medium than plating on the agar medium. Totally 42 isolates obtained from the wastes B23 and B42 showed highest antifungal activity against eight fungal pathogens such as Sclerotinia sclerotiorum, Rhizoctonia solani, Pythium ultimum, Phytophthora capsici, Fusarium oxysporum, Colletotrichum gloeosporioides, Cladosporium cucumerinum, and Botrytis cinerea and B23 and B42 were finally selected for further studies. Optimal concentration of the isolates was $10ml(10^7cfu/ml)$ to suppress the Sclerotinia rot of lettuce. Supplements such as starch, glycerol, and egg-yolk successfully maintained the bacterial population for 30 days in vitro and increased bio-control potentials against the disease. The bacterial isolate B23 alone showed 72% control value, furthermore it presented 95% control value when supplemented with 0.2% of starch, glycerol, and egg-yolk. The promising Bacillus isolates B23 and B42 were identified as Brevibacillus brevis and Bacillus stearothermophillus, respectively, based on morphological and physiological characteristics according to API database.

• Genomics & Informatics
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• v.5 no.1
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• pp.10-18
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• 2007

Numerous studies have reported that genes with similar expression patterns are co-regulated. From gene expression data, we have assumed that genes having similar expression pattern would share similar transcription factor binding sites (TFBSs). These function as the binding regions for transcription factors (TFs) and thereby regulate gene expression. In this context, various analysis tools have been developed. However, they have shortcomings in the combined analysis of expression patterns and significant TFBSs and in the functional analysis of target genes of significantly overrepresented putative regulators. In this study, we present a web-based A Functional Clustering Analysis Tool for Predicted Transcription Regulatory Elements and Gene Ontology Terms (FCAnalyzer). This system integrates microarray clustering data with similar expression patterns, and TFBS data in each cluster. FCAnalyzer is designed to perform two independent clustering procedures. The first process clusters gene expression profiles using the K-means clustering method, and the second process clusters predicted TFBSs in the upstream region of previously clustered genes using the hierarchical biclustering method for simultaneous grouping of genes and samples. This system offers retrieved information for predicted TFBSs in each cluster using $Match^{TM}$ in the TRANSFAC database. We used gene ontology term analysis for functional annotation of genes in the same cluster. We also provide the user with a combinatorial TFBS analysis of TFBS pairs. The enrichment of TFBS analysis and GO term analysis is statistically by the calculation of P values based on Fisher’s exact test, hypergeometric distribution and Bonferroni correction. FCAnalyzer is a web-based, user-friendly functional clustering analysis system that facilitates the transcriptional regulatory analysis of co-expressed genes. This system presents the analyses of clustered genes, significant TFBSs, significantly enriched TFBS combinations, their target genes and TFBS-TF pairs.

• The Journal of Society for e-Business Studies
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• v.18 no.2
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• pp.175-189
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• 2013

In this paper, an rice intake management system based on ubiquitous computing technology is introduced for rice processing complex (RPC). This system plays an important role in the quality management for rough rices in that the system provides timely and useful information of rice cultivation. The intake management system is developed by utilizing widespread ubiquitous technologies, such as smartphones, GIS and LBS, for the purpose of controling the harvest time and monitoring the quality of paddy. The information for rice production, cultivation and quality management is transmitted and stored in a centralized database via mobile networks, On the basis of these information, the harvest schedule is determined and notified to farmers though smart devices. Hence, the proposed system can help to establish trust among farmers, operators and consumers by providing systematic information based on ubiquitous computing technology.

• Journal of Internet of Things and Convergence
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• v.6 no.3
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• pp.67-73
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• 2020

The research status of endangered amphibians in Korea was mainly studied the life-cycle and distribution status of species from the 1980s to the early 2000s. Although a relatively diverse range of studies have been conducted on mackerels, studies on habitat prediction, analysis, change and management are insufficient. WEB, which provides biota information using location information in Korea, is a site operated by the National Bio Resource Center under the Ministry of Environment, but there is no information on endangered species and general species information has also been found to be very scantily. For this research, we secured a database of location information of Narrow-mouth frog, an endangered species, by combining literature and field research, and established a system by applying new technologies and open-based platform technologies that can be easily accessed by non-technical personnel of IT among IT technologies. The system was divided into administrator functions and user functions to prevent indiscriminate sharing of information through authentication procedures through user membership of users. The established system was authorized to show the distance between the current location and the location of the Narrow-mouth frog. Considering the ecological characteristics of the Narrow-mouth frog, which is an endangered species, a radius of 500m was marked to determine the habitat range. The system is expected to be applied to the legal system to change existing protected areas, etc. and to select new ones. It is estimated that practical reduction measures can be derived by utilizing the development plan for reviewing the natural environment. In addition, the deployed system has the advantage of being able to apply to a wide variety of endangered species by modifying the information entered.

• Molecules and Cells
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• v.39 no.12
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• pp.898-908
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• 2016

Despite recent groundbreaking advances in multiple myeloma (MM) treatment, most MM patients ultimately experience relapse, and the relapse biology is not entirely understood. To define altered gene expression in MM relapse, gene expression profiles were examined and compared among 16 MM patients grouped by 12 months progression-free survival (PFS) after autologous stem cell transplantation. To maximize the difference between prognostic groups, patients at each end of the PFS spectrum (the four with the shortest PFS and four with the longest PFS) were chosen for additional analyses. We discovered that integrin-${\alpha}8$ (ITGA8) is highly expressed in MM patients with early relapse. The integrin family is well known to be involved in MM progression; however, the role of integrin-${\alpha}8$ is largely unknown. We functionally overexpressed integrin-${\alpha}8$ in MM cell lines, and surprisingly, stemness features including $HIF1{\alpha}$, VEGF, OCT4, and Nanog, as well as epithelial mesenchymal transition (EMT)-related phenotypes, including N-cadherin, Slug, Snail and CXCR4, were induced. These, consequently, enhanced migration and invasion abilities, which are crucial to MM pathogenesis. Moreover, the gain of integrin-${\alpha}8$ expression mediated drug resistance against melphalan and bortezomib, which are the main therapeutic agents in MM. The cBioPortal genomic database revealed that ITGA8 have significant tendency to co-occur with PDGFRA and PDGFRB and their mRNA expression were up-regulated in ITGA8 overexpressed MM cells. In summary, integrin-${\alpha}8$, which was up-regulated in MM of early relapse, mediates EMT-like phenotype, enhancing migration and invasion; therefore, it could serve as a potential marker of MM relapse and be a new therapeutic target.

• Journal of Animal Science and Technology
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• v.45 no.5
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• pp.731-738
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• 2003

The technique known as proteomics is useful for characterizing the protein expression pattern of a particular tissue or cell type as well as quantitatively identifying differences in the levels of individual proteins. In present study, we carried out the comparative expression patterns of white and red muscles. We used the two-dimensional electrophoresis(2-DE) for analyzing the protein expression. Proteins isolated from porcine white and red muscles were separated by 12% poly-acrylamide gel and then were detected by coomassie blue and silver staining. More than 600 protein spots were detected on each 2-DE gel. By visual analysis of the stained gel, five proteins were identified to be differentially expressed in the white vs red muscle. By database searching based on the molecular weights and pI(isoelectric point) of the five proteins, three of them were found to be most close to troponin I, T and myoglobin. However, further researche is needed for identification and functional analysis of the unidentified proteins. In conclusion, we found five proteins, which are differentially expressed in the white vs red muscle. The functional analysis of the differentially expressed proteins will provide valuable information on biochemical characteristics of the muscle type.

• Journal of Digital Convergence
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• v.14 no.3
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• pp.235-241
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• 2016

Among recent issues emerging in the areas related to the society, health has received the most attention. In this paper, for a patient unable to do self-care because of worsened diseases, a biological information transfer method is proposed by which the disease information can be securely managed, by attaching an implantable device into the body. Our method object of the invention is to prevent a third party from illegally intercepting and interfering with the biological information attached to the insertion device in the body. In the proposed technique to improve the safety of the patient between the hospital and physician by assigning each code to the biometric information of the patient in order to prevent a third party tapping and interfering. In addition, our method is assigned a code necessary for encoding in advance to confirm the biological information between the patient and the hospital (doctor) in a manner dividing the bio-information code. In particular, the proposed technique makes a third party unable to illegally tap or interfere in, by previously generating a code used for encoding so that it can be stored in the database of the hospital, which not only decreased hospital care time to 6.9%, but also increased work efficiency rate up to 12.7%.