• Korean Journal of Ichthyology
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• v.23 no.2
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• pp.95-105
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• 2011

To explain the origin of the Korean mandarin fish (Siniperca scherzeri), phylogenetic relationships and DNA polymorphism among Siniperca fishes have been investigated based on mitochondrial cytochrome b DNA sequences. As a result, S. roulei were firstly differentiated early in the evolution of Siniperca fishes and the other six species (S. schezeri, S. undulata, S. fortis, S. obscura, S. knerii and S. chuatsi) were evolved slightly later. However, the order of species differentiation among six species was not clear because the nodes of their phylogeny were poorly resolved. The constructed molecular phylogeny revealed three genetically distinct groups of local populations of S. scherzeri. The first group (group 1) is the local populations of Korean peninsula and northern China including Lioaning and Henan. The second one (group 2) is the local populations of Anhui, Fujian and Guangxi. The third one (group 3) is the local population of Zhejiang. The number of nucleotide differences in base pairs were 31~43 between group 1 and 2; 37~44 between group 2 and 3; 27~29 between group 1 and 3; and 1~5 within group 1. Thus, the Korean mandarin fish was likely to be originated from the northern China local population which was isolated from the middle or southern China local populations during the Cenozoic Pliocene. Low level of sequence divergence between Korean mandarin fish populations and northern China population indicated a recent expansion of distribution ranges from northern China to Korean peninsula.

• Korean Journal of Microbiology
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• v.32 no.4
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• pp.245-251
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• 1994

Ten strains of 7 species from the genus Ganoderma, G. lucidum ATCC 64251, FP-103561-T, and ES70701, G. applanatum ATCC 44053 and FP-57035-T. G. lobatum ATCC 42985, G. resinaceum ATCC 52416, G. subamboinense var. laevisporum ATCC 52420, G. meredithae ATCC 64492, and G. microsporum ATCC 76024, were studied to discuss their phylogenetic relationships by utilizing restriction fragment length polymorphisms (RFLPs) of mitochondrial DNAs (mtDNAs). Six restriction enzymes, BamHI, BglII, EcoRI, HindIII, PvuII, and XbaI which digested mtDNAs into adequate numbers of restriction fragments for cluster analysis, were used in this study. Restriction profiles of strains for each restriction enzyme were treated as analysis characters to calculate similarity coefficients, which were converted into nucleotide sequence divergence values whose mean values were then arranged in a matrix table. This table was utilized for a phylogenetic analysis using the Neighborjoining method of the PHYLIP package to construct phylogenetic tree. Three strains of G. lucidum and two strains of G. applanatum exhibited different lineages each but one of G. applanatum strains showed a close relationship with G. lobatum, which reflected the species complexity of these species whose strains were phenotypically indistinguishable but genetically distinct. The present results suggest that the natural classification of Ganoderma needs to be considered from the viewpoints of molecular biology-based systematics as well as morphological classifications and cultural identifications for better phylogenetic conclusions.

• Korean Journal of Ichthyology
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• v.33 no.2
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• pp.107-116
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• 2021

Two stone loaches (Nemacheilidae, Cypriniformes), Barbatula toni (Dybowski, 1869) and B. nuda (Bleeker, 1864), have been recognized in the Korean waters to date. Recently, due to indiscriminate artificial introduction as well as the change of their habitats induced by natural disasters, it seems to be concerned about the damage of species-specific geographic boundaries. We examined the genetic difference of two Korean Barbatula species by the haplotype network based on the Cytochrome b sequences of mitochondrial DNA and the phylogenetic relationships among them including Barbatula fishes occurring around the Korean peninsula. As a result, three and 29 haplotypes were obtained from B. toni and B. nuda, respectively, and totally three clades comprising "toni group", "nuda hangang group", and "nuda donghae group" were identified. The sequence variable sites among them was 10~24%, showing a difference of interspecific level. Phylogenetic relationships of the latter group, especially, forms an independent cluster discriminating with other two groups as well as the Chinese, Japanese, Russian, and European Barbatula species, suggesting the possibility of the specific level divergence.

• Fisheries and Aquatic Sciences
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• v.27 no.3
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• pp.145-158
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• 2024

Life history characteristics, habitat landscape, and historical events are believed to have shaped the patterns of genetic variation in many taxa. The bony lip barb, Osteohilus vittatus, represent a potamodromous fish that complete all life cycle in freshwater and is widely distributed in Southeast Asia. It usually lives in small rivers and other freshwater habitats, and movement between habitats for either food or reproduction has been typical. These life history characteristics may promote gene flow, leading to less structured populations. However, many freshwater habitats are fragmented, which restricts gene flow. We investigate how this interplay has shaped patterns of genetic variation and phylogeographic structure within this species in the Sundaland, a biodiversity hotspot with a complex geological history, using mitochondrial cytochrome oxidase I (mtCOI) as a genetic marker. Forty-six mtCOI sequences of 506 bp long were collected from ten localities, eight geographically isolated and two connected. The sequences were used for population genetic and phylogeographic analyses. Our results showed a low genetic diversity within populations but high between populations. There was a deep phylogeographic structure among geographically isolated populations but a lack of such structure in the connected habitats. Among geographically isolated populations, sequence divergence was revealed, ranging from 1.8% between Java and Sumatra populations to 12.2% between Malaysia and Vietnam. An indication of structuring was also observed among localities that are geographically closer but without connectivity. We conclude that despite high dispersal capacity, the joint effects of historical events, long-term geographic isolation associated with sea level oscillation during the Pleistocene, and restricted gene flow related to lack of habitat connectivity have shaped the phylogeographic structure within the O. vittatus over the Sundaland.

• Journal of Life Science
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• v.20 no.3
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• pp.336-344
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• 2010

To assess population structure and genetic diversity among the Pacific cod (Gadus macrocephalus), we investigated mtDNA COI gene sequences of 7 populations. Samples were obtained from Sokcho, Wolsung, Geojedo, Yeosu, Geomundo and Westsouth in 2008 and 2009 (n=28). The sequence analysis of 28 individual samples showed 8 haplotypes, ranging in sequence divergence by pairwise comparisons from 0.2 to 2.2% (1 bp-11 bp). The Gal haplotype was found in Wolsung, Geojedo, Yeosu, Geomundo and Westsouth, and was regarded as the main haplotype of Korean Pacific cod. Ga2, Ga3, Ga6 and Ga7 haplotypes were found only in Sokcho. In the PHYLIP analysis, 8 haplotypes formed two independent groups: cladeA consisted of Ga2, Ga3, Ga6 and Ga7 haplotypes, whereas cladeB contained Gal, Ga4, Ga5 and Ga8 haplotypes. The genetic relationship between the two groups was weakly supported by bootstrap analysis(<50%). In pairwise comparisons between 6 populations other than that from Sokcho, a very high per generation migration ratio ($N_m$=infinite) and a very low level of geographic distance ($F_{sr}=-0.0123-(-0.0423)$) were observed. The estimates of genetic distance between Sokcho and the other localities were all statistically significant (p<0.05, p<0.01, p<0.001), indicating a limited mtDNA-based gene flow between Sokcho and other regions. The finding of the lowest genetic diversity in the Sokcho population (nucleotide diversity=0.00589) may be a result of relatively small population size and interrupted gene flow to other localities. Consequently, the overall considerable migration of Pacific cod population in Korea caused a genetically homogeneous structure to form, although a distinct population was found in this study.

• The Korean Journal of Nuclear Medicine
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• v.38 no.6
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• pp.486-491
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• 2004

Purpose: factor analysis and independent component analysis (ICA) has been used for handling dynamic image sequences. Theoretical advantages of a newly suggested ICA method, ensemble ICA, leaded us to consider applying this method to the analysis of dynamic myocardial $H_2^{15}O$ PET data. In this study, we quantified patients' blood flow using the ensemble ICA method. Materials and Methods: Twenty subjects underwent $H_2^{15}O$ PET scans using ECAT EXACT 47 scanner and myocardial perfusion SPECT using Vertex scanner. After transmission scanning, dynamic emission scans were initiated simultaneously with the injection of $555{\sim}740$ MBq $H_2^{15}O$. Hidden independent components can be extracted from the observed mixed data (PET image) by means of ICA algorithms. Ensemble learning is a variational Bayesian method that provides an analytical approximation to the parameter posterior using a tractable distribution. Variational approximation forms a lower bound on the ensemble likelihood and the maximization of the lower bound is achieved through minimizing the Kullback-Leibler divergence between the true posterior and the variational posterior. In this study, posterior pdf was approximated by a rectified Gaussian distribution to incorporate non-negativity constraint, which is suitable to dynamic images in nuclear medicine. Blood flow was measured in 9 regions - apex, four areas in mid wall, and four areas in base wall. Myocardial perfusion SPECT score and angiography results were compared with the regional blood flow. Results: Major cardiac components were separated successfully by the ensemble ICA method and blood flow could be estimated in 15 among 20 patients. Mean myocardial blood flow was $1.2{\pm}0.40$ ml/min/g in rest, $1.85{\pm}1.12$ ml/min/g in stress state. Blood flow values obtained by an operator in two different occasion were highly correlated (r=0.99). In myocardium component image, the image contrast between left ventricle and myocardium was 1:2.7 in average. Perfusion reserve was significantly different between the regions with and without stenosis detected by the coronary angiography (P<0.01). In 66 segment with stenosis confirmed by angiography, the segments with reversible perfusion decrease in perfusion SPECT showed lower perfusion reserve values in $H_2^{15}O$ PET. Conclusions: Myocardial blood flow could be estimated using an ICA method with ensemble learning. We suggest that the ensemble ICA incorporating non-negative constraint is a feasible method to handle dynamic image sequence obtained by the nuclear medicine techniques.