• 생명과학회지
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• 제14권1호
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• pp.57-60
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• 2004

육종재료를 얻기 위하여 부산ㆍ경남지역에서 수집된 우리나라 재래종 옥수수 49계통에 대하여 주성분분두법을 이용하여 계통간 거리를 구하였고, 이를 이용하여 계통분류를 실시하였던 바 다음과 같은 결과를 얻었다. 계통간 거리에 의해 49계통은 4개의 계통군으로 분류되었고, 계통군 I 에는 11계통, 계통군 II에는 20계통, 계통군 III에 는 14계통, 그리고 계통군 IV에는 4계통이 속하였다. 계통군 I은 조생, 단간, 소수, 소분얼형의 계통들이었고, 계통군 II는 조생, 장간, 대수, 다수, 소분얼형의 계통이었고, 계통군 III은 만생, 단간, 소수, 다분얼형 의 계통이었고, 계통군 IV는 중생, 장간, 대수, 다수, 다분얼형의 계통들이었다.

• 한국생물정보학회:학술대회논문집
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• 한국생물정보시스템생물학회 2003년도 제2차 연례학술대회 발표논문집
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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.

• 천문학회보
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• 제41권2호
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• pp.49.1-49.1
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• 2016

Asteroid taxonomy dates back to the mid-1970's and is based mostly on broadband photometric and spectroscopic observations in the visible wavelength. Different taxonomic classes have long been characterized by spectral slope shortward of 0.75 microns and the absorption band in 1 micron, the principal components. In this way, taxonomic classes are grouped and divided into four broad complexes; silicates (S), carbonaceous (C), featureless (X), Vestoids (V), and the end-members that do not fit well within the S, C, X and V complexes. The past decade witnessed an explosion of data due to the advent of large-scale asteroid surveys such as SDSS. The classification scheme has recently been expanded with the analysis of the SDSS 4th Moving Object Catalog (MOC 4) data. However, the boundaries of each complex and subclass are rather ambiguously defined by hand. Furthermore, there are only few studies on asteroid taxonomy using Johnson-Cousins filters, and those were conducted on a small number of objects, with significant uncertainties. In this paper, we present our preliminary results for a new taxonomic classification of asteroids using SMASS, Bus and DeMeo (2014) and the SDSS MOC 4 datasets. This classification scheme is simply represented by a triplet of photometric colors, either in SDSS or in Johnson-Cousins photometric systems.

• ALGAE
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• 제34권1호
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• pp.57-70
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• 2019

DNA metabarcoding is currently used for large-scale taxonomic identification to understand the community composition in various marine ecosystems. However, before being widely used in this emerging field, this experimental and analytic approach still has several technical challenges to overcome, such as polymerase chain reaction (PCR) bias, and lack of well-established metabarcoding markers, a task which is difficult but not impossible to achieve. In this study, we present an adapted PCR-free small-organelles enriched metagenomics (SoEM) method for marine biodiversity assessment. To avoid PCR bias and random artefacts, we extracted target DNA sequences without PCR amplification from marine environmental samples enriched with small organelles including mitochondria and plastids because their genome sequences provide a valuable source of molecular markers for phylogenetic analysis. To experimentally enrich small organelles, we performed subcellular fractionation using modified differential centrifugation for marine environmental DNA samples. To validate our SoEM method, two marine environmental samples from the coastal waters were tested the taxonomic capturing capacity against that of traditional DNA metabarcoding method. Results showed that, regardless of taxonomic levels, at least 3-fold greater numbers of taxa were identified in our SoEM method, compared to those identified by the conventional multi-locus DNA metabarcoding method. The SoEM method is thus effective and accurate for identifying taxonomic diversity and presents a useful alternative approach for evaluating biodiversity in the marine environment.

• Journal of Microbiology
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• 제34권2호
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• pp.117-123
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• 1996

Restriction-polymorphic patterns of nuclear-ITS were examined for the genetic relationships among 12 bisidiomycetous mushrooms to Aphyllophorales and Agaricales. The taxonomic affinity of Ganoderma species with the family Polyporaceae also was examined. With 13 restriction endonucleases, 159 restriction characters were generated form the 12 species examined. UPGMA and neighbor-joining analyses separated the 12 species into two genetically distinct groups that correspond to orders (Agaricales and Aphyllophorales) where each species is included. This result indicates that there is clear genetic demarcation between Agaricales and Aphyllophorales. Dendrograms constructed by several data analyses showed that even though Ganoderma species are somewhat in intermediate taxonomic position between the Polyporaceae and families of the Agaricales, they are genetically more related to the Polyporaceae. These results are consistent with morphological characters observed in those mushrooms. However, it is premature to conclude taxonomic status Ganoderma species in the present study employing small sample size.

• Journal of Plant Biology
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• 제31권2호
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• pp.83-89
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• 1988

The Fucales plants have very homogenous taxonomic characteristics at order level, but show many morphological variatations at species or subspecies levels. This study is one of the serial works to obtain more taxonomic data than morphotaxonomic ones and to clarify the taxonomic ranks and characteristics of Korean Fucales plants through physiological and biochemical analyses. Total lipid compositions of Korean Fucales plants were analyzed by the 3-dimensional TLC method. Major components of phospholipids (PA, PC, PG, PE, DPG, LPE, LPC), neutral fat TG and sterols were commonly contained in each species. Unknown lipids X1, X2 and X3 were contained in genus Sargassum, but Hizikia was lacking X3 and Myagropsis was lacking both X2 and X3. The latter contained unique X8. From the view-point of the phylogeny of lipid metabolism, Sargassum might be more closely related to Hizikia than to Myagropsis. A variant of S. patens from Seongsan showed minute metabolic difference from that of the typical plant; but a variant of S. serratifolium did not show any significant difference from that of the typical plant.

• 한국패류학회지
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• 제10권1호
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• pp.19-26
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• 1994

Eight species of the family Bithyniidae, Bithynia tentaculata, B. leachi, B. siaminsis, B manchourica, B misella, B. kiusiuensis, Gabbia australis and a Bithynia wp. collected from Nepal, were studied for their relationship between species. Total 20 characters were employed for the principal component analysis(PCA) and taxonomic distance. G. misella and B. kiusiuensis were closely related and similar to G. australis. B. manchourica, B. tentaculata and B. siamensis relatively closed group, and taxonomic distance of B. leachi was far from the other species.

• Mycobiology
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• 제36권4호
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• pp.203-210
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• 2008

In previous studies investigating the genus Xanthoparmelia, thirteen different species have been reported from South Korea alone. However, there currently has been no revisional study performed until now. To explore the genus Xanthoparmelia, a phenotypic analysis was performed based on morphological, anatomical and chemical characters, while an investigation of Xanthoparmelia phylogeny was based on nuclear ribosomal (nr) DNA ITS sequences. A thorough examination of the specimens deposited in the Korean Lichen Research Institute (KoLRI) confirmed that eight species of Xanthoparmelia occur inside South Korea. Our analysis further confirmed the colors of the lower surface and medullar chemistry are important taxonomic characters in Xanthoparmelia. This study also presents a detailed description of each species and a key to the genus.

• Proceedings of the National Institute of Ecology of the Republic of Korea
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• 제5권3호
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• pp.76-85
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• 2024

The purpose of this study is to propose a new method of analysis focusing on interconnections between species rather than traditional biodiversity analysis, which represents ecosystems in terms of species and individual counts such as species diversity and species richness. This new approach aims to enhance our understanding of ecosystem networks. Utilizing data from the 4th National Natural Environment Survey (2014-2018), the following eight taxonomic groups were targeted for our study: herbaceous plants, woody plants, butterflies, Passeriformes birds, mammals, reptiles & amphibians, freshwater fishes, and benthonic macroinvertebrates. A co-occurrence frequency analysis was conducted using nationwide data collected over five years. As a result, in all eight taxonomic groups, the degree value represented by a linear regression trend line showed a slope of 0.8 and the weighted degree value showed an exponential nonlinear curve trend line with a coefficient of determination (R²) exceeding 0.95. The average value of the clustering coefficient was also around 0.8, reminiscent of well-known social phenomena. Creating a combination set from the species list grouped by temporal information such as survey date and spatial information such as coordinates or grids is an easy approach to discern species distributed regionally and locally. Particularly, grouping by species or taxonomic groups to produce data such as co-occurrence frequency between survey points could allow us to discover spatial similarities based on species present. This analysis could overcome limitations of species data. Since there are no restrictions on time or space, data collected over a short period in a small area and long-term national-scale data can be analyzed through appropriate grouping. The co-occurrence frequency analysis enables us to measure how many species are associated with a single species and the frequency of associations among each species, which will greatly help us understand ecosystems that seem too complex to comprehend. Such connectivity data and graphs generated by the co-occurrence frequency analysis of species are expected to provide a wealth of information and insights not only to researchers, but also to those who observe, manage, and live within ecosystems.

• Animal Systematics, Evolution and Diversity
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• 제39권3호
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• pp.99-113
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• 2023

The nudibranch is one of the most colorful gastropod species found in oceans worldwide. Unlike many other gastropod groups, the nudibranch loses an external shell in the adult stage, but instead develops various chemical defense systems. More than 2,500 nudibranch species have been reported worldwide, and 73 species are currently recorded in Korean waters. In this study, we present morphological descriptions, DNA barcode information of mtDNA cox1 sequence, and taxonomic review for five nudibranch species: Apata pricei (MacFarland, 1966), Doto rosacea Baba, 1949, Janolus toyamensis Baba and Abe, 1970, Polycera abei (Baba, 1960), and Trinchesia sibogae (Bergh, 1905). Of these, we also provide in-depth discussion of taxonomic issue of A. pricei that was previously subdivided into two subspecies, A. pricei pricei and A. pricei komandorica. Our morphological examination and molecular analyses of the mtDNA cox1 sequences indicate that these two subspecies are not taxonomically warranted. The phylogenetic information for the other nudibranch species from mtDNA cox1 sequence analysis is also included, providing a molecular basis for species identification and inferring their local phylogenies within each of the species groups discussed herein.