• 식물분류학회지
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• 제50권3호
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• pp.333-342
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• 2020

Despite poorly documented species delimitation and unresolved taxonomic nomenclature, four species of Symplocos (S. coreana, S purnifolia, S sawafutagi, and S. tanakana) have been described in Korea. In this study, we carried a comparative wood anatomy analysis of all four species of Korean Symplocos to understand the wood anatomical variations among them. The results of this study indicated that Korean Symplocos are comparatively indistinguishable in terms of their qualitative wood features, except for exclusively uniseriate rays present in S. purnifolia instead of uniseriate to multiseriate in other three species. Nevertheless, differences are noticed in quantitative wood variables such as the vessel density, vessel size, and ray density. The vessel density of S. purnifolia is more than twice as high as those of S. sawafutagi and S. tanakana. In contrast, the vessel circumference and diameter on both plants of S. sawafutagi and S. tanakana is nearly twice as large as those of S. purnifolia. Symplocos coreana has characteristic intermediacy between these two groups in terms of vessel features and is closer to S. purnifolia in terms of its ray density level. A cluster analysis based on a paired group (unweighted pair-group method with the arithmetic mean, UPGMA) algorithm using the Euclidean similarity index clearly differentiates S. purnifolia from the remaining species, representing the first branch of the phenogram.

• Journal of Ecology and Environment
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• 제34권3호
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• pp.323-331
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• 2011

Biodiversity and the community composition of micro-eukaryotic organisms were investigated in the Upo wetland in Korea using molecular analysis. Molecular identification was performed using cytochrome oxidase I (COI) and small subunit ribosomal DNA (SSU rDNA). The genomic DNA was isolated directly from soil samples. The COI and SSU rDNA regions were amplified using universal primers and then sequenced after cloning. In a similarity search of the obtained sequences with BLAST in the Genbank database, the closely related sequences from NCBI were used to identify the amplified sequences. A total of six eukaryotic groups (Annelida, Arthropoda, Rotifera, Chlorophyta, Bacillariophyta, and Stramenopiles) with COI and six groups (Annelida, Arthropoda, Rotifera, Alveolata, Fungi, and Apicomplexa) with SSU rDNA genes were determined in the Upo wetland. Among 38 taxa in 20 genera, which are closely related to the amplified sequences, 10 genera (50%) were newly reported in Korea and five genera (25%) were shown to be distributed in the Upo wetland. This approach is applicable to the development of an efficient method for monitoring biodiversity without traditional taxonomic processes and is expected to produce more accurate results in depositing molecular barcode data in the near future.

• 한국생물정보학회:학술대회논문집
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• 한국생물정보시스템생물학회 2000년도 International Symposium on Bioinformatics
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• pp.17-20
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• 2000

Structural genomics aims to provide a good experimental structure or computational model of every tractable protein in a complete genome. Underlying this goal is the immense value of protein structure, especially in permitting recognition of distant evolutionary relationships for proteins whose sequence analysis has failed to find any significant homolog. A considerable fraction of the genes in all sequenced genomes have no known function, and structure determination provides a direct means of revealing homology that may be used to infer their putative molecular function. The solved structures will be similarly useful for elucidating the biochemical or biophysical role of proteins that have been previously ascribed only phenotypic functions. More generally, knowledge of an increasingly complete repertoire of protein structures will aid structure prediction methods, improve understanding of protein structure, and ultimately lend insight into molecular interactions and pathways. We use computational methods to select families whose structures cannot be predicted and which are likely to be amenable to experimental characterization. Methods to be employed included modern sequence analysis and clustering algorithms. A critical component is consultation of the presage database for structural genomics, which records the community's experimental work underway and computational predictions. The protein families are ranked according to several criteria including taxonomic diversity and known functional information. Individual proteins, often homologs from hyperthermophiles, are selected from these families as targets for structure determination. The solved structures are examined for structural similarity to other proteins of known structure. Homologous proteins in sequence databases are computationally modeled, to provide a resource of protein structure models complementing the experimentally solved protein structures.

• 한국수산과학회지
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• 제28권6호
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• pp.699-707
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• 1995

Eurasian yellow perch (Perca fluviatilis) and American yellow perch (Perca flavescens) are known to be endemic species in Eurasia and North America, respectively. The presence of endemic species on each continent suggests their independent evolutionary history. However, because of the morphological similarity, distribution pattern, and only recent fossil record, their divergence time and speciation of the two Perca species has long been controversial. Here, from the comparison of the entire nucleotide sequences of cytochrome b gene, large genetic divergence between the two Perca species is observed although they are morphologically similar each other. Among 1,140 base pairs, interspecific nucleotide differences are found at 130 sites $(11.4\%)$. The differences varies with codon position, showing 22 sites in the first, 5 sites in the second, and 103 sites in the third codon position. Considering the types of nucleotide changes, transitional differences are much more than transversional differences and its ratio turned out to be 5.19. The estimated divergence time of the two Perca species indicates that they were separated each other approximately in the late Miocene period, which implies the long history of speciation. With comparison of the inferred amino acid sequences, strong structural and functional constraints which seem to be maintained by the highly conservative amino acid residues or protein regions, as found in other taxonomic groups of organisms, are also recognized in the cytochrome b of the fishes examined.

• 한국미생물학회:학술대회논문집
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• 한국미생물학회 2002년도 추계학술대회
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• pp.81-85
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• 2002

Oligotrophic bacteria isolated from forest soil showed a specific community consisting of various taxonomic groups compared with those in other soil or aquatic habitats. Based on the cell shape, the isolates were divided into four groups: regular rod, curved/spiral rod, irregular rod, and prosthecate bacteria. The cellular fatty acids 60 oligotrophic isolates were analyzed. At the dendrogram based on cellular fatty acid composition, four clusters(I-IV) were separated at a euclidian distance of about 50. Based on the 16S rDNA sequence analysis, the two representative strains(MH256 and MA828) of cluster 3 showed the close relation to genera, Xathomonas/Stenotrophomonas, but were not included in these genera. The isolates with Q-10 were also studied. They are corresponded to the two large groups in Proteobacteria alpha subdivision. One was incorporated in the genus Bradyrhizobium cluster, which also includes Agromonas, a genus for oligotrophic bacteria. The strains of the other group showed high similarity to the genus Agrobacterium. We attempted to screening of bioactive compounds from oligotrophs which was isolated from forest soil. The active compounds were analyzed by mass and NMR spectrum, one of them identified as crisamicin A. Another one designated as SAPH is a new compound. The results indicate that there were possibilities for finding new compounds from the rare microorganisms such as oligotrophs.

• 미생물학회지
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• 제43권2호
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• pp.137-141
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• 2007

Streptomyces 5균주 간의 유사도를 혈청학적 방법으로 측정하였다. 항원으로는 충분히 생장한 균체의 외피를 Tween 20으로 용출시킨 용액을 사용하였고 항체는 토끼를 면역시켜 얻었다. 면역확산과 ELISA 결과 항원-항체 반응의 정도가 균주간의 분류학적 유사성과 비례적으로 반영되지 않았다. 즉 군집 A에 속하는 균주들 사이의 항원-항체 반응이 낮게 측정된 반면에 군집 F의 Streptomyces Iavendulae와 군집 A의 Streptomyces viridochromogenes가 특이적으로 비교적 높게 나타났다.

• Ocean Science Journal
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• 제40권3호
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• pp.155-166
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• 2005

New PCR primers (N=18) were designed for the isolation of complete SSU to LSU rDNA sequences from the dinoflagellate Alexandrium tamarense. Standard PCR, employing each primer set selected for amplifications of less than 1.5 kb, successfully amplified the expected rDNA regions of A. tamarense (Korean isolate, HY970328M). Complete SSU, LSU rDNAs and ITS sequences, including 5.8S rDNA, were recorded at 1,800 bp, 520 bp and 3,393 bp, respectively. The LSU rDNA sequence was the first report in Alexandrium genus. No intron was found in the LSU rRNA coding region. Twelve D-domains within the LSU rDNA were put together into 1,879 bp (44.4% G+C), and cores into 1514 bp (42.8% G+C). The core sequence was significantly different (0.0867 of genetic distance, 91% sequence similarity) in comparison with Prorocentrum micans (GenBank access. no. X16108). The D2 region was the longest in length (300 bp) and highly variable among the 12 D-domains. In a phylogenetic analysis using complete LSU rDNA sequences of a variety of phytoplankton, A. tamarense was clearly separated with high resolution against other species. The result suggests that the sequence may resolve the taxonomic ambiguities of Alexandrium genus, particularly of the tamarensis complex.

• Journal of Species Research
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• 제5권2호
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• pp.235-240
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• 2016

To investigate the indigenous prokaryotic species diversity in Korea, various environmental samples from diverse ecosystems were examined taxonomically. The isolated bacterial strains were identified based on 16S rRNA gene sequences, and those exhibiting at least 98.7% sequence similarity with known bacterial species but never reported in Korea were selected as unrecorded species. As an outcome of this study, 10 unrecorded bacterial species belonging to the phylum Firmicutes were discovered from various sources such as soil, tidal flat, fresh water, sea water, kimchi and gut of Fulvia mutica. The unrecorded species were assigned to 7 different genera of 5 families, namely Bacillus and Ornithinibacillus of Bacillaceae, Exiguobacterium of Exiguobacteriaceae, Brevibacillus and Paenibacillus of Paenibacillaceae, Staphylococcus of Staphylococcaceae, and Lactococcus of Streptococcaceae. The selected isolates were subjected to further taxonomic characterization including the analysis of Gram reaction, cellular and colonial morphology, biochemical activities, and phylogenetic trees. The descriptive information on the 10 unrecorded species are provided.

• Animal Systematics, Evolution and Diversity
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• 제2권1호
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• pp.63-78
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• 1986

Two species of Moroco oxycephalus and M. lagowskii were studied to examine patterns of genic variation and morphological difference within and between populations of two species, and to clarify their taxonomic status and geographic distribution. The number of scales above lateral line(SAL) was the key character to classify these species. On the average, M.lagowskii had 22 or more SAL whereas M.oxycephalus had 20 or less. Previously known character of the position of dorsal fin was found to be not appropriate to distinguish them. Five loci, Gp, st-1, Est-2, Est-3 and Got-1 , showed fixed difference electrophoretically between two species and these could be used as genetic markers to identify them. The degree of genic variation of M. oxycephalus was four fold higher(H=0.032) than that of M. lagowskii(H=0.008) but both species were far less than the average genic variation of freshwater fish in general. Rogers' genetic similarity coefficients between two species were S=0.692 and their presumed divergent time was estimated to be sbout 1.8million years ageo. Detailed survey of the geographic distribution of thses revealed that M.lagowskii was distributed in northeastern part of South Korea(Ganseong , Gangreung, Wangsan, and Oggye) and M. oxycephalus was occupied rest of the peninsula. The distrance between Oggye, the southern limit of M. lagowskii distribution , and Samwha (near Samcheog), the northern limit of M.oxycephalus, was aobut 15 Km apart and no symparty was found in between.

• 한국미생물·생명공학회지
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• 제49권3호
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• pp.384-390
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• 2021

A Gram-negative, aerobic, motile by gliding, and rod-shaped marine bacterium, designated CE67^T was isolated from the marine sponge Callyspongia elegans on Biyang-do in Jeju Island. The CE67^T strain grew optimally at 25℃, pH 7.5, and in the presence of 2-3% (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequence showed that strain CE67^T was related to the genus Aureivirga and had the highest 16S rRNA gene sequence similarity to the Aureivirga marina VIII.04^T type strain (96.3%). The primary fatty acids (>10%) of strain CE67^T were iso-C_15:0 (35.3%) and iso-C_17:0 3OH (21.8%). The polar lipid profile of strain CE67^T contained phosphatidylethanolamine, unidentified aminolipids, and unidentified lipids. The predominant menaquinone was MK-6. The DNA G+C content was 29.1 mol%. Based on the polyphasic taxonomic analysis, strain CE67^T was determined to be a representative novel species of the genus Aureivirga for which we propose the name Aureivirga callyspongiae sp. nov., whose strain type is CE67^T (=KCTC 42847^T=JCM 34566^T).