• Korean Journal of Plant Taxonomy
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• v.40 no.2
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• pp.118-129
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• 2010

A taxonomic study of Viola albida complex, containing the representative individuals of three taxa, V. albida var. albida, V. albida var. chaerophylloides, and V. albida var. takahashii, was done based on RAPD data. The amplified loci were 476 in total; obtained with 68 universal primers on seven OTUs. Nei's genetic dissimilarity appeared relatively low within individuals of V. albida var. albida and V. albida var. chaerophylloides (0.118-0.171 and 0.051 respectively), however, it was higher in individuals of V. albida var. takahashii (0.348). On the other hand, there is no specific trend in terms of genetic dissimilartiy among taxa, such as between individuals of V. albida var. albida and V. albida var. takahashii, between those of V. albida var. albida and V. albida var. chaerophylloides, and between those of V. albida var. albida and V. albida var. takahashii. The similarity of OTUs studied is high in clustering analysis, so that this result is compatible with the establishment of this complex. All OTUs are clustered within two groups. The individuals of V. albida var. takahashii, however, are clustered both to the group of V. albida var. albida and to the group of V. albida var. chaerophylloides, meaning that the genetic difference is high which would be commensurate with their morphological variations.

• Journal of KIISE:Databases
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• v.37 no.3
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• pp.127-136
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• 2010

With rapid growth of information and computer communication technologies, the numbers of digital documents including multimedia data have been recently exploded. In particular, news video database and news video mining have became the subject of extensive research, to develop effective and efficient tools for manipulation and analysis of news videos, because of their information richness. However, many research focus on browsing, retrieval and summarization of news videos. Up to date, it is a relatively early state to discover and to analyse the plentiful latent semantic knowledge from news videos. In this paper, we propose the news video mining system based on multi-modal approach and text mining, which uses the visual-textual information of news video clips and their scripts. The proposed system systematically constructs a taxonomy of news video stories in automatic manner with hierarchical clustering algorithm which is one of text mining methods. Then, it multilaterally analyzes the topics of news video stories by means of time-cluster trend graph, weighted cluster growth index, and network analysis. To clarify the validity of our approach, we analyzed the news videos on "The Second Summit of South and North Korea in 2007".

• Korean Journal of Plant Taxonomy
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• v.49 no.2
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• pp.118-126
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• 2019

The taxonomic rank of the tiny-leaved terrestrial orchid Cephalanthera subaphylla Miyabe & $Kud{\hat{o}}$ has been somewhat controversial, as it has been treated as a species or as an infraspecific taxon, under C. erecta (Thunb.) Blume [C. erecta var. subaphylla (Miyabe & $Kud{\hat{o}}$) Ohwi and C. erecta f. subaphylla (Miyabe & $Kud{\hat{o}}$) M. Hiro]. Allozyme markers, traditionally employed for delimiting species boundaries, are used here to gain information for determining the taxonomic status of C. subaphylla. To do this, we sampled three populations of five taxa (a total of 15 populations) of Cephalanthera native to the Korean Peninsula [C. erecta, C. falcata (Thunb.) Blume, C. longibracteata Blume, C. longifolia (L.) Fritsch, and C. subaphylla]. Among 20 putative loci resolved, three were monomorphic (Dia-2, Pgi-1, and Tpi-1) across the five species. Apart from C. longibracteata, there was no allozyme variation within the remaining four species. Of the 51 alleles harbored by these 17 polymorphic loci, each of the 27 alleles at 14 loci was unique to a single species. Accordingly, we found low average values of Nei's genetic identities (I) between ten species pairs (from I = 0.250 for C. erecta versus C. longifolia to I = 0.603 for C. falcata vs. C. longibracteata), with C. subaphylla being genetically clearly differentiated from the other species (from I = 0.349 for C. subaphylla vs. C. longifolia to 0.400 for C. subaphylla vs. C. falcata). These results clearly indicate that C. subaphylla is not genetically related to any of the other taxa of Cephalanthera that are native to the Korean Peninsula, including C. erecta. In a principal coordinate analysis (PCoA), C. subaphylla was positioned distant not only from C. falcata, C. longibracteata, and C. longifolia, but also from C. erecta. Finally, K = 5 was the best clustering scheme using a Bayesian approach, with five clusters precisely corresponding to the five taxa. Thus, our allozyme results strongly suggest that C. subaphylla merits the rank of species.

• Korean Journal of Plant Taxonomy
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• v.44 no.4
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• pp.250-256
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• 2014

This study was carried out to understand the genetic relationship of three Aloe spp. cultivated in Korea, A. saponaria, A. vera and A. arborescens and a new variant in Korea based on three plastid (matK, trnL-F, rbcL) and one nuclear (ITS regions) DNA barcode markers. A total of 2,420 bp sequence was amplified. Two indels were detected in the trnL region, and also several species specific nucleotide loci were detected in all 29 parsimonious informative sites, and 148 variable sites were detected among four taxa studied while 170 variable and 75 parsimonious sites were detected when other Aloe spp. in worldwide were used. An UPGMA phenogram with 10,000 bootstrap replication showed that the new variant was closest to A. vera. The variant was not morphologically and genetically concurrent with any reported species so far. The clustering of Aloe species were broadly in agreement with previously reported results.

• Korean Journal of Plant Taxonomy
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• v.49 no.4
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• pp.324-333
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• 2019

Neutral genetic diversity found in plant species usually leaves an indelible footprint of historical events. Korea's main mountain range (referred to as the Baekdudaegan [BDDG]), is known to have served as a glacial refugium primarily for the boreal and temperate flora of northeastern Asia. In addition, life-history traits (life forms, geographic range, and breeding systems) influence the within- and among-population genetic diversity of seed plant species. For example, selfing species harbor significantly less within-population genetic variation than that of predominantly outcrossers. A previous study of two Liparis species (L. makinoana and L. kumokiri) emphasizes the role of the abovementioned factors shaping the levels of genetic diversity. Liparis makinoana, mainly occurring on the BDDG and self-incompatible, harbors high levels of within-population genetic diversity (expected heterozygosity, H_eP = 0.319), whereas there is no allozyme variation (H_eP = 0.000) in L. kumokiri, which is self-compatible and mainly occurs in lowland hilly areas. To determine if this trend is also found in other congeners, we sampled five populations of L. krameri from the southern part of the Korean Peninsula and investigated the allozyme-based genetic diversity at 15 putative loci. The somewhat intermediate levels of within-population genetic variation (H_eP = 0.145) found in L. krameri are most likely due to its occurrence in mountainous areas that, despite being outside of the main ridge of the BDDG, still served as refugia, and a self-incompatible breeding system. Management strategies are suggested for L. krameri and L. makinoana based on the levels and distribution of genetic diversity and inbreeding.

• Journal of Microbiology and Biotechnology
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• v.30 no.9
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• pp.1355-1366
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• 2020

Sediment bacterial communities are critical to the biogeochemical cycle in river ecosystems, but our understanding of the relationship between sediment bacterial communities and their specific input streams in rivers remains insufficient. In this study, we analyzed the sediment bacterial community structure in a local river receiving discharge of urban domestic sewage by applying Illumina MiSeq high-throughput sequencing. The results showed that the bacterial communities of sediments samples of different pollution types had similar dominant phyla, mainly Proteobacteria, Actinobacteria, Chloroflexi and Firmicutes, but their relative abundances were different. Moreover, there were great differences at the genus level. For example, the genus Bacillus showed statistically significant differences in the hotel site. The clustering of bacterial communities at various sites and the dominant families (i.e., Nocardioidaceae, and Sphingomonadaceae) observed in the residential quarter differed from other sites. This result suggested that environmentally induced species sorting greatly influenced the sediment bacterial community composition. The bacterial co-occurrence patterns showed that the river bacteria had a nonrandom modular structure. Microbial taxonomy from the same module had strong ecological links (such as the nitrogenium cycle and degradation of organic pollutants). Additionally, PICRUSt metabolic inference analysis showed the most important function of river bacterial communities under the influence of different types of domestic sewage was metabolism (e.g., genes related to xenobiotic degradation predominated in residential quarter samples). In general, our results emphasize that the adaptive changes and interactions in the bacterial community structure of river sediment represent responses to different exogenous pollution sources.

• Journal of Plant Biotechnology
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• v.39 no.3
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• pp.121-126
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• 2012

To determine whether FT-IR spectroscopy combined with multivariate analysis for whole cell extracts can be used to discriminate major leguminous plant at metabolic level, seed extracts of six leguminous plants were subjected to Fourier transform infrared spectroscopy (FT-IR). FT-IR spectral data from seed extracts were analyzed by principal component analysis (PCA), partial least square discriminant analysis (PLS-DA) and hierarchical clustering analysis (HCA). The PCA could not fully discriminate six leguminous plants, however PLS-DA could successfully discriminate six leguminous plants. The hierarchical dendrogram based on PLS-DA separated the six leguminous plants into four branches. The first branch was consisted of all three Vigna species including Vigna radiata var. radiate, Vigna angularis var. angularis and Vigna unguiculata subsp. Unguiculata. Whereas Pisum sativum var. sativum, Glycine max L and Phaseolus vulgaris var. vulgaris were clustered into a separate branch respectively. The overall results showed that metabolic discrimination system were in accordance with known phylogenic taxonomy. Thus we suggested that the hierarchical dendrogram based on PLS-DA of FT-IR spectral data from seed extracts represented the most probable chemotaxonomical relationship between six leguminous plants.

• Journal of Marine Life Science
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• v.8 no.1
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• pp.43-49
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• 2023

This study applied a metagenomic analysis of the penguins' gut microbiome from fecal samples of Adélie Penguin (Pygoscelis adeliae) and Emperor Penguin (Aptenodytes forsteri) living along the Ross Sea, Antarctica. As a result of taxonomic analysis, 7 phyla and 18 families were mainly present in the gut microbiome of Adélie and Emperor penguins. To assess microbial diversity, we performed alpha diversity and OTU abundance analyses. It was confirmed that the Adélie Penguin's gut microbial species had a higher diversity than Emperor Penguin's. Based on the Beta diversity analysis using PCoA, differences were observed in the clustering between Adélie and Emperor penguins, respectively. Through the KEGG pathway analysis using PICRUSt, the nucleoside and nucleotide biosynthesis pathway was the most prevalent in Adélie and Emperor penguins. This study enabled a comparison and analysis of the composition and diversity of the gut microbiome in Adélie and Emperor Penguins. It could be utilized for future research related to penguin feeding habits and could serve as a foundation for analyzing the gut microbiomes of various other Antarctic organisms.

• Journal of Intelligence and Information Systems
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• v.19 no.1
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• pp.111-123
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• 2013

Semantic similarity/relatedness measure between two concepts plays an important role in research on system integration and database integration. Moreover, current research on keyword recommendation or tag clustering strongly depends on this kind of semantic measure. For this reason, many researchers in various fields including computer science and computational linguistics have tried to improve methods to calculating semantic similarity/relatedness measure. This study of similarity between concepts is meant to discover how a computational process can model the action of a human to determine the relationship between two concepts. Most research on calculating semantic similarity usually uses ready-made reference knowledge such as semantic network and dictionary to measure concept similarity. The topological method is used to calculated relatedness or similarity between concepts based on various forms of a semantic network including a hierarchical taxonomy. This approach assumes that the semantic network reflects the human knowledge well. The nodes in a network represent concepts, and way to measure the conceptual similarity between two nodes are also regarded as ways to determine the conceptual similarity of two words(i.e,. two nodes in a network). Topological method can be categorized as node-based or edge-based, which are also called the information content approach and the conceptual distance approach, respectively. The node-based approach is used to calculate similarity between concepts based on how much information the two concepts share in terms of a semantic network or taxonomy while edge-based approach estimates the distance between the nodes that correspond to the concepts being compared. Both of two approaches have assumed that the semantic network is static. That means topological approach has not considered the change of semantic relation between concepts in semantic network. However, as information communication technologies make advantage in sharing knowledge among people, semantic relation between concepts in semantic network may change. To explain the change in semantic relation, we adopt the cognitive semantics. The basic assumption of cognitive semantics is that humans judge the semantic relation based on their cognition and understanding of concepts. This cognition and understanding is called 'World Knowledge.' World knowledge can be categorized as personal knowledge and cultural knowledge. Personal knowledge means the knowledge from personal experience. Everyone can have different Personal Knowledge of same concept. Cultural Knowledge is the knowledge shared by people who are living in the same culture or using the same language. People in the same culture have common understanding of specific concepts. Cultural knowledge can be the starting point of discussion about the change of semantic relation. If the culture shared by people changes for some reasons, the human's cultural knowledge may also change. Today's society and culture are changing at a past face, and the change of cultural knowledge is not negligible issues in the research on semantic relationship between concepts. In this paper, we propose the future directions of research on semantic similarity. In other words, we discuss that how the research on semantic similarity can reflect the change of semantic relation caused by the change of cultural knowledge. We suggest three direction of future research on semantic similarity. First, the research should include the versioning and update methodology for semantic network. Second, semantic network which is dynamically generated can be used for the calculation of semantic similarity between concepts. If the researcher can develop the methodology to extract the semantic network from given knowledge base in real time, this approach can solve many problems related to the change of semantic relation. Third, the statistical approach based on corpus analysis can be an alternative for the method using semantic network. We believe that these proposed research direction can be the milestone of the research on semantic relation.

• Development and Reproduction
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• v.10 no.4
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• pp.227-238
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• 2006

Genomic DNAs(gDNAs) were isolated from the venus clam(Gomphina aequilatera) from Samcheok(venus clam from Samcheok; VCS) and Wonsan(venus clam from Wonsan; VCW) located in the East Sea of the Korean Peninsula. The amplified products were generated by agarose gel electrophoresis(AGE) with oligonucleotides primer, detected by staining with ethidium bromide and viewed by ultraviolet ray. The seven arbitrarily selected primers BION-21, BION-23, BION-25, BION-27, BION-29, BION-31 and BION-33 generated the shared loci, polymorphic, and specific loci, with the molecular sizes ranging from 150 bp to 2,400 bp. In this study, 147 polymorphic loci(147/954 loci, 15.41%) in VCS population and 274(274/996 loci, 27.51%) in VCW population were generated with seven primers. These results suggest the genetic variation in VCW population is higher than in VCS population. Especially, the 700 bp bands generated by the primer BION-21 were identified commonly in two Gomphina populations, which identified populations and/or species. This specific primer was found to be useful in the identification of individuals and/or population, resulting from the different DNA polymorphism among individuals/species/population. Two Gomphina populations between the individual SAMCHEOK no. 03 and WONSAN no. 22 showed the longest genetic distance(0.696) in comparison with other individuals used. The complete linkage cluster analysis indicating three genetic groupings and dendrogram revealed close relationships among individual identities within two geographical populations of venus clam(G. aequilatera) from the Samcheok and Wonsan. The intra-species classification and clustering analyses inferred from molecular markers supported the traditional taxonomy of the species based on morphological characters such as shell size, shape and color. Accordingly, as mentioned above, RAPD analysis showed that VCS population was more or less separated from VCW population.