• Journal of Microbiology and Biotechnology
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• v.26 no.11
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• pp.1863-1870
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• 2016

Antimicrobial peptides/proteins (AMPs) are present in all types of organisms, from microbes and plants to vertebrates and invertebrates such as insects. The grasshopper Oxya chinensis sinuosa is an insect species that is widely consumed around the world for its broad medicinal value. However, the lack of available genetic information for this species is an obstacle to understanding the full potential of its AMPs. Analysis of the O. chinensis sinuosa transcriptome and expression profile is essential for extending the available genetic information resources. In this study, we determined the whole-body transcriptome of O. chinensis sinuosa and analyzed the potential AMPs induced by bacterial immunization. A high-throughput RNA-Seq approach generated 94,348 contigs and 66,555 unigenes. Of these unigenes, 36,032 (54.14%) matched known proteins in the NCBI database in a BLAST search. Functional analysis demonstrated that 38,219 unigenes were clustered into 5,499 gene ontology terms. In addition, 26 cDNAs encoding novel AMPs were identified by an in silico approach using public databases. Our transcriptome dataset and AMP profile greatly improve our understanding of O. chinensis sinuosa genetics and provide a huge number of gene sequences for further study, including genes of known importance and genes of unknown function.

• Korean Journal of Computational Design and Engineering
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• v.19 no.4
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• pp.390-401
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• 2014

ISO 15926 is an international standard for integration of lifecycle data for process plants including oil and gas facilities. From the viewpoint of information modeling, ISO 15926 Parts 2 provides the general data model that is designed to be used in conjunction with reference data. Reference data are standard instances that represent classes, objects, properties, and templates common to a number of users, process plants, or both. ISO 15926 Parts 4 and 7 provide the initial set of classes, objects, properties and the initial set of templates, respectively. User-defined reference data specific to companies or organizations are defined by inheriting from the initial reference data and the initial set of templates. In order to support the extension of reference data and templates, an editor that provides creation, deletion and modification functions of user-defined reference data is needed. In this study, an editor for reference data based on ISO 15926 was developed. Sample reference data were encoded in OWL (web ontology language) according to the specification of ISO 15926 Part 8. iRINGTools and dot15926Editor were benchmarked for the design of GUI (graphical user interface). Reference data search, creation, modification, and deletion functions were implemented with XML (extensible markup language) DOM (document object model), and SPARQL (SPARQL protocol and RDF query language).

• Environmental Analysis Health and Toxicology
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• v.26
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• pp.10.1-10.7
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• 2011

Objects: Chironomus riparius, a non-biting midge (Chironomidae, Diptera), is extensively used as a model organism in aquatic ecotoxicological studies, and considering the potential of C. riparius larvae as a bio-monitoring species, little is known about its genome sequences. This study reports the results of an Expressed Sequence Tags (ESTs) sequencing project conducted on C. riparius larvae using 454 pyrosequencing. Method: To gain a better understanding of C. riparius transcriptome, we generated ESTs database of C.ripairus using pyrosequencing method. Results: Sequencing runs, using normalized cDNA collections from fourth instar larvae, yielded 20,020 expressed sequence tags, which were assembled into 8,565 contigs and 11,455 singletons. Sequence analysis was performed by BlastX search against the National Center for Biotechnology Information (NCBI) nucleotide (nr) and uniprot protein database. Based on the gene ontology classifications, 24% (E-value${\leq}1^{-5}$) of the sequences had known gene functions, 24% had unknown functions and 52% of sequences did not match any known sequences in the existing database. Sequence comparison revealed 81% of the genes have homologous genes among other insects belonging to the order Diptera providing tools for comparative genome analyses. Targeted searches using these annotations identified genes associated with essential metabolic pathways, signaling pathways, detoxification of toxic metabolites and stress response genes of ecotoxicological interest. Conclusions: The results obtained from this study would eventually make ecotoxicogenomics possible in a truly environmentally relevant species, such as, C. riparius.

• Journal of Korea Multimedia Society
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• v.10 no.2
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• pp.147-169
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• 2007

Semantic Web Services Discovery matches between users' requirements and the ontological description of Web Services. However, concepts of an ontology can be interpreted differently according to a point of view. Previous works are limited in interpreting concepts. Since they lack a precise scheme of describing the advertisements and requirements of services and users, respectively, and even do not support a sophisticated matching, semantic mismatches may occur. This paper presents a sophisticated method of discovering Web services. The proposed method facilitates specifying semantics precisely and flexibly based on a proposed integrated concept model. Additionally, more sophisticated discovery is supported by computing complex matchings with many-to-many relationships. Experimental results show that the proposed method performs more efficiently for various kinds of user requests, compared with previous works.

• Journal of the Korea Institute of Information and Communication Engineering
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• v.11 no.9
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• pp.1771-1780
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• 2007

The necessity of Information integration has emphasized by advancement of internet and change of enterprise environment. In enterprises, it usually integrates the multi-database constructing by M&A. For this integration of information it must guarantee interpretation and integration which is stabilized with solving heterogeneous characteristic problem. In this paper, we propose the method that change the global XML query to local XML query for interpretation. It is based on XMDR(eXtended Meta-Data Registry) which expresses the connection between the standard and the local for solve the interoperability problem in heterogeneous environment. Thus, we propose the legacy model that can search and modify by one Query with creating global XML Query by XMDR. and for his, we use the 2PC technique which is the distributed transaction control technique of existing.

• Korean Journal of Agricultural Science
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• v.45 no.4
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• pp.583-590
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• 2018

Genus Typha L. (Typhaceae; Cattail in common) is one of the hydrophytic plants found in semi-aquatic regions. About nine to 18 species of the genus exist all over the world. In Korea, the most commonly found cattail species are T. laxmanni and T. angustifolia. The aim of this study was to prepare a cDNA library and sequences and analyze expressed sequence tags (ESTs) from these species, T. laxmanni and T. angustifolia. In the case of T. laxmanni, we observed that 715 out of 742 ESTs had high quality sequences, whereas the remaining 27 ESTs were low quality sequences. In this study, we identified 77 contigs, 393 unassembled clones and 65.7% singletons. Furthermore, in the case of T. angustifolia, we recorded 992 high quality EST sequences, and by excluding 28 low quality sequences from among them, we retrieved 120 contigs, 348 unassembled clones and 48.9% singletons. The basic local alignment search tool (BLAST) and Kyoto encyclopedia of genes and genomes (KEGG) database results enabled us to identify the functional categories, i.e., molecular function (16.5%), biological process (22.2%) and cellular components (61.3%). In addition, between these two species, the no hits and anonymous genes were 4.2% and 11.7% and 6.2% and 11.2% in T. laxmanni and T. angustifolia, respectively, based on the BLAST results. The study concluded that they have certain species-specific genes. Hence, the results of this study on these two species could be a valuable resource for further studies.

• Journal of Ginseng Research
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• v.43 no.4
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• pp.666-675
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• 2019

Background: Korean Red Ginseng (KRG) has been widely used as an herbal medicine to normalize and strengthen body functions. Although many researchers have focused on the biological effects of KRG, more studies on the action mechanism of red ginseng are still needed. Previously, we investigated the proteomic changes of the rat spleen while searching for molecular signatures and the action mechanism of KRG. The proteomic analysis revealed that differentially expressed proteins (DEPs) were involved in the increased immune response and phagocytosis. The aim of this study was to evaluate the biological activities of KRG, especially the immune-enhancing response of KRG. Methods: Rats were divided into 4 groups: 0 (control group), 500, 1000, and 2000 mg/kg administration of KRG powder for 6 weeks, respectively. Isobaric tags for relative and absolute quantitation was performed with Q-Exactive LC-MS/MS to compare associated proteins between the groups. The putative DEPs were identified by a current UniProt rat protein database search and by the Gene Ontology annotations. Results: The DEPs appear to increase the innate and acquired immunity as well as immune cell movement. These results suggest that KRG can stimulate immune responses. This analysis refined our targets of interest to include the potential functions of KRG. Furthermore, we validated the potential molecular targets of the functions, representatively LCN2, CRAMP, and HLA-DQB1, by Western blotting. Conclusion: These results may provide molecular signature candidates to elucidate the mechanisms of the immune response by KRG. Here, we demonstrate a strategy of tissue proteomics for the discovery of the molecular function of KRG.

• Journal of Korean Neurosurgical Society
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• v.65 no.5
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• pp.697-709
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• 2022

Objective : The present study aimed to identify the function of ischemic stroke (IS) patients' peripheral blood and its role in IS, explore the pathogenesis, and provide direction for clinical research progress by comprehensive bioinformatics analysis. Methods : Two datasets, including GSE58294 and GSE22255, were downloaded from Gene Expression Omnibus database. GEO2R was utilized to obtain differentially expressed genes (DEGs). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis of DEGs were performed using the database annotation, visualization and integrated discovery database. The protein-protein interaction (PPI) network of DEGs was constructed by search tool of searching interactive gene and visualized by Cytoscape software, and then the Hub gene was identified by degree analysis. The microRNA (miRNA) and miRNA target genes closely related to the onset of stroke were obtained through the miRNA gene regulatory network. Results : In total, 36 DEGs, containing 27 up-regulated and nine down-regulated DEGs, were identified. GO functional analysis showed that these DEGs were involved in regulation of apoptotic process, cytoplasm, protein binding and other biological processes. KEGG enrichment analysis showed that these DEGs mediated signaling pathways, including human T-cell lymphotropic virus (HTLV)-I infection and microRNAs in cancer. The results of PPI network and cytohubba showed that there was a relationship between DEGs, and five hub genes related to stroke were obtained : SOCS3, KRAS, PTGS2, EGR1, and DUSP1. Combined with the visualization of DEG-miRNAs, hsa-mir-16-5p, hsa-mir-181a-5p and hsa-mir-124-3p were predicted to be the key miRNAs in stroke, and three miRNAs were related to hub gene. Conclusion : Thirty-six DEGs, five Hub genes, and three miRNA were obtained from bioinformatics analysis of IS microarray data, which might provide potential targets for diagnosis and treatment of IS.

• Korean Journal of Heritage: History & Science
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• v.57 no.1
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• pp.6-19
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• 2024

The Korean Archaeological Dictionary, which represents Korean archaeological knowledge information, contains refined and high-quality information written by expert collective intelligence. This is a characteristic that clearly distinguishes it from overseas archaeological data archives, and can be called differentiated infrastructure data. However, it has not played a role as an information service or knowledge information platform reflecting the latest digital technology. As a way to maximize these strengths and compensate for weaknesses, it was proposed to develop and operate a GIS-based knowledge and information platform for Korean archaeology. To realize this, it is necessary to develop a title management system centered on repositories and metadata that can collect and store various information, link open linked data design and related systems, develop a search function that can analyze and visualize data in response to the big data era, and establish a WebGIS-based information service system. This will be a platform to continuously manage, supplement, and update Korean archaeological knowledge information, build a ubiquitous environment where anyone can use information anytime, anywhere, and create various types of business models.

• Proceedings of the Korea Contents Association Conference
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• 2006.11a
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• pp.218-222
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• 2006

In making 3D animation with digital technology, it is necessary to increase productivity and reusability by managing production pipeline systematically through standardization of animation content. For this purpose, we try to develop the animation content management system that can manage all kind of information on the production pipeline, based on SCORM of e-teaming by considering production, publication and re-editing. A scene as the unit of visual semantics is standardize into an object that contains meta-data of place, cast, weather, season, time and viewpoint about the scene. The meta-data of content includes a lot of information of copyright, publication, description, etc, so that it plays an important role on the management and the publication. If an effective management system of meta-data such as ontology will be implemented, it is possible to search multimedia contents powerfully. Hence, it will bring on production and publication of UCC. Using the meta-data of content object, user and producer can easily search and reuse the contents. Hence, they can choose the contents object according to their preference and reproduce their own creative animation by reorganizing and packaging the selected objects.