• Korean Journal of Microbiology
• /
• v.49 no.2
• /
• pp.184-190
• /
• 2013

Cave environment provides special ecosystems for evolution of lives distant from surface environments. We investigated bacterial and archaeal communities of wall biofilm obtained from of a volcanic cave (Daesubee) in Jeju, Republic of Korea. Bacterial and archaeal 16S rRNA genes were PCR-amplified and sequenced using pyrosequencing technologies. Unique prokaryotic communities with low diversities were observed. The main bacterial sequences (ca. 83% of total reads) were affiliated with Pseudonocardia mongoliensis of phylum Actinobacteria and clustered with clones obtained from various caves. Reflection of light on the wall surface of cave might be caused by formation of beads of water caused by hydrophobic filaments of actinobacterial colonies. Main archaeal sequences (ca. 65.7% of total reads) were related with those of I.1a-Associated group of phylum Thaumarchaeota. The sequences were related with that of Candidatus Nitrosotalea devanaterra which was known to oxidize ammonia under acidic condition (ca. pH 5.0). Nutrients leached through volcanic soils contribute formation of unique microbial communities of wall biofilm of cave Daesubee.

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

• Journal of the Korean Society for information Management
• /
• v.33 no.3
• /
• pp.133-154
• /
• 2016

Interdisciplinary approach has been recognized as one of key strategies to address various and complex research problems in modern science. The purpose of this study is to investigate the interdisciplinary characteristics and structure of the field of big data. Among the 1,083 journals related to the field of big data, multiple Subject Categories (SC) from the Web of Science were assigned to 420 journals (38.8%) and 239 journals (22.1%) were assigned with the SCs from different fields. These results show that the field of big data indicates the characteristics of interdisciplinarity. In addition, through bibliographic coupling network analysis of top 56 journals, 10 clusters in the network were recognized. Among the 10 clusters, 7 clusters were from computer science field focusing on technical aspects such as storing, processing and analyzing the data. The results of cluster analysis also identified multiple research works of analyzing and utilizing big data in various fields such as science & technology, engineering, communication, law, geography, bio-engineering and etc. Finally, with measuring three types of centrality (betweenness centrality, nearest centrality, triangle betweenness centrality) of journals, computer science journals appeared to have strong impact and subjective relations to other fields in the network.

• Journal of KIISE
• /
• v.41 no.9
• /
• pp.652-665
• /
• 2014

Many important terminologies in biomedical text are expressed as abbreviations or acronyms. We newly suggest a semantic link topic model based on the concepts of topic and dependency link to disambiguate biomedical abbreviations and cluster long form variants of abbreviations which refer to the same senses. This model is a generative model inspired by the latent Dirichlet allocation (LDA) topic model, in which each document is viewed as a mixture of topics, with each topic characterized by a distribution over words. Thus, words of a document are generated from a hidden topic structure of a document and the topic structure is inferred from observable word sequences of document collections. In this study, we allow two distinct word generation to incorporate semantic dependencies between words, particularly between expansions (long forms) of abbreviations and their sentential co-occurring words. Besides topic information, the semantic dependency between words is defined as a link and a new random parameter for the link presence is assigned to each word. As a result, the most probable expansions with respect to abbreviations of a given abstract are decided by word-topic distribution, document-topic distribution, and word-link distribution estimated from document collection though the semantic dependency link topic model. The abstracts retrieved from the MEDLINE Entrez interface by the query relating 22 abbreviations and their 186 expansions were used as a data set. The link topic model correctly predicted expansions of abbreviations with the accuracy of 98.30%.

• Korean Journal of Social Welfare
• /
• v.65 no.2
• /
• pp.313-334
• /
• 2013

A study aims to assess Korean mental health literacy and analyze the characteristics of vulnerable population. This study presented typical vignettes of schizophrenia, depression and alcoholism to 1,197 adults randomly. All respondents were asked for recognition of mental illness, beliefs about causes, professional help and self-help, stigma for receiving psychiatric treatment for the person described. The results showed that the recognition of mental health problem in a vignette was very poor and that personal causes were seen by public as more important than environmental and bio-genetic causes. When the public were asked about various professional therapies and self-help activities, psychotherapy was favored while other professional help were considered to be less helpful than self-help activities. Among professionals, psychiatrist were viewed as most helpful. We used cluster analysis to compare high mental health literacy group with low mental health literacy group(vulnerable population). Vulnerable population were found to be more aged and to live in county area. We proposed government initiated program for enhancing public mental health literacy.

• Journal of Life Science
• /
• v.27 no.6
• /
• pp.694-701
• /
• 2017

Mycoplasma genitalium represents the smallest genome among mono-cultivable prokaryotes. To discover and compare the orthologs (conservative genes) among M. genitalium and 14 prokaryotes that are uncultivable and have less orthologs than M. genitalium, COG (clusters of orthologous groups of protein) analyses were applied. The analyzed prokaryotes were M. genitalium, one hyperthermophilic exosymbiotic archaeon Nanoarchaeum equitans, four intracellular plant pathogenic eubacteria of Candidatus Phytoplasma genus, and nine endosymbiotic eubacteria of phloem- and xylem-feeding insects. Among 367 orthologs of M. genitalium, 284 orthologs were conservative between M. genitalium and at least one other prokaryote. All 15 prokaryotes commonly have 29 orthologs, representing the significance of proteins in life. They belong to 25 translation-related, including 22 ribosomal proteins, 3 subunits of RNA polymerase, and 1 protein-folding-related. Among the 15 prokaryotes, 40 orthologs were only found in all four Candidatus Phytoplasma. The other nine Candidatus, all endosymbionts with insects, showed only a single common COG0539 (ribosomal protein S1), representing the diversity of orthologs among them. These results might provide clues to understand conservative genes in uncultivable prokaryotes, and may be helpful in industrial areas, such as handling prokaryotes producing amino acids and antibiotics, and as precursors of organic synthesis.

• Korean Journal of Ecology and Environment
• /
• v.34 no.3 s.95
• /
• pp.185-191
• /
• 2001

The morphological variation and density of the Euglena viridis cells and environmental factors of urban waterways of Daejoncheon , Jeonjucheon, Kwangjucheon, Kumhogang, Mihocheon,and Musimcheon, Korea were studied from 25December, 1995 to 5 January, 1997 in order toelucidate possible relationships among the bio-logical and abiological factors. All E. viridis cells were same in having single star-cluster of chlo-roplast lobes and included two morphotypes based on other detailed morphology. The morphotype I cells agreed well with the typical form off. viridrs and commonly occurred in most of waters and bloomed with $5386\;cells\;{\cdot}\;mL^{-1}$ in Kwangjucheon. The density of the morphotype Ipositively correlated with ammonium (r = 0.80)and nitrite (r = 0.68), while negatively with nit-rate concentration. The morphotype II cells were characterized by having randomly scattered cytoplasmic granules beneath pellicle and unevenmargined lobes of chloroplasts. The density of the morphotype II positively correlated with nitrate (r = 0.98), while negatively correlated with ammonium and nitrite. However, the density of each morphotype was not significantly related with inorganic phosphate, temperature and pH of surface water. These results indicate that E. viridis includes two morphotypes in urban waterways in Korea, that coexist in the same period and station as a response of allocation of nitrogenous nutrients.

• Korean Journal of Microbiology
• /
• v.45 no.2
• /
• pp.105-111
• /
• 2009

Norovirus (NV) with a variety of genotypes, a member of the family Caliciviridae, causes acute nonbacterial gastroenteritis in humans. We determined the nucleotide sequence of three open reading frames (ORFs) of a NV Korean strain and characterized the genetic relationship with others. The Korean strain designated Hu/NLV/Gunpo/2006/KO was isolated from the stool specimen of a 2-year-old female suffering from gastroenteritis. By performing reverse transcription and PCR amplification, three overlapping cDNAs were synthesized and used for direct sequencing. We found that like other NVs, this strain contains three ORFs: ORF1, 5,100 bp; ORF2, 1,647 bp; ORF3, 765 bp. Of 35 NVs, ORF1 had a level of genetic diversity lower than ORF2 and ORF3, of which the C-termini of the ORF2 and ORF3 showed a relatively high degree of genetic diversity. Phylogenetic analyses indicated that the Korean strain belonged to genogroup II, with Saitama U1, Gifu'96, Mc37, and Vietnam 026 being formed a single genetic cluster. The nucleotide sequence information of three ORFs of a NV Korean isolate will be useful not only for the development of a diagnostic tool and understanding of genetic relationship, but also provide important basic information for the functional analysis of their gene products.

• The Journal of Korean Institute of Communications and Information Sciences
• /
• v.36 no.12B
• /
• pp.1450-1458
• /
• 2011

The HPcN (Hybrid & high Performance Convergence Network) in research networks means environment which can provide both computing resource such as supercomputer, cluster and network resource to application researchers in the field of medical, bio, aerospace and e-science. The most representative research network in Korea, KREONET has been developing following technologies through the HERO (Hybrid Networking project for research oriented infrastructure) from 200S. First, we have constructed and deployed a control plane technology which can provide a connection oriented network dynamically. Second, the integrated resource management system technology has been developing for reservation and allocation of both computing and network resources, whenever users want to utilize them. In this paper, a testbed network is presented, which is possible to reserve and allocate network resource using the integrated resource management system. We reserve network resource through GNSI (Grid Network Service Interface) messages between GRS (Global Resource Scheduler) and NRM (Network Resource Manager) and allocate network resource through GUNI (Grid User Network Interface) messages between the NRM (network resource manager) and routers, based on reservation information provided from a user on the web portal. It is confirmed that GUNI interface messages are delivered from the NRM to each router at the starting of reservation time and traffic is transmitted through LSP allocated by the NRM.

• Polymer(Korea)
• /
• v.35 no.2
• /
• pp.161-165
• /
• 2011

This study is related to the preparation of biocompatible gold nanoparticles (AuNPs) which are stable in aqueous solutions for a long time. Ultrasmall polyethyleneimine (PEI)-capped AuNPs (PEI-AuNPs) with limited agglomeration were prepared in aqueous solutions at room temperature, which were based on the roles of PEI as a reductant and a stabilizer. PEI-AuNPs with an average size of 8~12 nm formed highly stable nanocolloids with an average hydrodynamic cluster size of around 50 nm in aqueous media. At a low concentration of metal precursor hydrogen tetrachloroaurate (III), the particle size was reduced noticeably. The typical peaks of gold were observed in the X-ray diffraction pattern of AuNPs. The cell viability of 98% was obtained in the case of PEI-AuNPs, while PEI was cytotoxic. The PEI-AuNP is considered to be a potential candidate as a contrast agent for computed tomography.