• Ocean and Polar Research
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• v.36 no.2
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• pp.189-197
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• 2014

The pearl-spot damsel, Chromis notata, is one of the important fishery species in Korea. While C. notata has been commonly harvested in southern Korea, the increasing number of C. notata in higher latitudes has crucial ecological, economic and evolutionary implications under conditions where the climate is rapidly changing. Here we examined the morphological and genetic characteristics of C. notata to assess patterns of geographical variations among the groups from three different sites. The groups were clearly distinguishable in the analysis of morphological characteristics. On the other hand, the groups were genetically indistinguishable. All individuals fell within a single clade in the neighbor-joining tree but appeared scattered in the haplotype network. Several haplotypes are shared among the sampling sites (Jejudo-Ulleungdo; Hap 9, Wangdolcho-Ulleungdo; Hap 28, Hap 33, Hap 34). Although control region markers did not elucidate the spatial patterns in genetic characteristics, Wangdolcho and Ulleungdo groups appear to exhibit a more robust gene flow between the two groups than with Jejudo group. Integrative approaches such as those combining morphological and genetic analyses minimize potential errors caused by limited perspectives of each analysis and can provide useful information for discovering functional DNA regions attributable to morphological characteristics expressions.

• Animal cells and systems
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• v.6 no.2
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• pp.167-170
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• 2002

The long terminal repeats (LTRs) of human endogenous retrovirus (HERV) have been found to be coexpressed with sequences of closely located genes. It has been suggested that the LTR elements have contributed to the structural change or genetic variation of human genome connected to various diseases and evolution. We examined the HERV-W LTR elements in various cancer cells (2F7, A43l , A549, HepG2, MIA-PaCa-2, PC-3, RT4, SiHa, U-937, and UO-31). Using genomic DNA from the cancer cells, we performed PCR amplification and identified twelve new HERV-W LTR elements. Those LTR elements showed a high degree of sequence similarity (88-99％) with HERV-W LTR (AF072500). A phylogenetic tree obtained by the neighbor-joining method revealed that HERV-W LTR elements could be mainly divided into two groups through evolutionary divergence. Three HERV-W LTR elements (RT4-2, A43l-1, and UO3l-2) belonged to Group 1, whereas nine LTR elements (2F7-2, A549-1, A549-3, HepG2-3, MP2-2, PC3-1, SiHa-8, SiHa-10, and U937-1) belonged to Group 11. Taken together, our new sequence data of the HERV-W LTR elements may contribute to an understanding of tissue-specific cancer by genomic instability of LTR integration.

• Journal of Aquaculture
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• v.22 no.1
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• pp.83-91
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• 2009

The Korean doty barbel Hemibarbus mylodon (Cypriniformes; Cyprinidae) is a critically endangered freshwater fish species mainly because of its natural habitat degradation. Three full-length complementary DNA (cDNA) clones representing different muscle actin isoforms were isolated and characterized. The three muscle actin isoforms were 1,294-1,601 bp long with the identical open reading frames of 1,134 bp with the deduced amino acid residues of 377. They showed 83.9-87.2% identities in the coding nucleotide level and 96.8-98.1% identities in the amino acid level. Phylogenetic analysis with the coding nucleotide sequences revealed that three muscle actin isoforms of H. mylodon formed strongly supported monophyletic groups with one of cypriniform skeletal $\alpha$-actin (acta1), cypriniform aortic $\alpha$-actins (acta2), and uncharacterized Danio rerio muscle actin isoform/Salmo trutta slow muscle actin (a novel muscle actin type). Our phylogenetic tree further suggested that cypriniform acta2 only showed the orthologous relationship to tetrapod acta2. Other multiple actin isoforms from diverse teleostean taxa were however clustered to no tetrapod orthologs, i.e., acta1, cardiac $\alpha$-actins (aetc1), acta2, and enteric $\gamma$-actin (actg2). This result strongly suggested that teleostean muscle actins have experienced different and complicated evolutionary history in comparison to mammalian counterparts.

• Journal of the Society of Naval Architects of Korea
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• v.42 no.5 s.143
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• pp.534-541
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• 2005

Until now, Korean shipyards have accumulated a great amount of data. But they do not have appropriate tools to utilize the data in practical works. Engineering data contains experts' experience and know-how in its own. It is very useful to extract knowledge or information from the accumulated existing data by using data mining technique This paper treats an evolutionary computation based on genetic programming (GP), which can be one of the components to realize data mining. The paper deals with linear models of GP for the regression or approximation problem when given learning samples are not sufficient. The linear model, which is a function of unknown parameters, is built through extracting all possible base functions from the standard GP tree by utilizing the symbolic processing algorithm. In addition to a standard linear model consisting of mathematic functions, one variant form of a linear model, which can be built using low order Taylor series and can be converted into the standard form of a polynomial, is considered in this paper. The suggested model can be utilized as a designing tool to predict design parameters with small accumulated data.

• Animal cells and systems
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• v.5 no.2
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• pp.133-137
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• 2001

Long terminal repeats (LTRs) of the human endogenous retrovirus K family (HERV-K) have been found to be coexpressed with sequences of genes closely located nearby. We examined transcribed HERV-K LTR elements in human brain tissue. Using cDNA synthesized from mRNA of the human brain, we performed PCR amplification and identified ten HERV-K LTR elements. These LTR elements showed a high degree of sequence similarity (92.4-99.7%) with the human-specific LTR elements. A phylogenetic tree obtained by the neighbor-joining method revealed that HERV-K LTR elements could be divided into two groups through evolutionary divergence. Some HERV-K LTR elements (HKL-B7, HKL-B8, HKL-B10) belonging to the group II from human brain cDNA were closely related to the human-specific HERV-K LTR elements. Our data suggest that HERV-K LTR element are active in the human brain; they could conceivably play a pathogenic role in human diseases such as psychosis.

• Journal of Life Science
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• v.24 no.6
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• pp.626-632
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• 2014

The genetic structure and phylogenetic relationship were investigated in Korean red spotted grouper populations using the nucleotide sequence polymorphisms of the mitochondrial DNA (mtDNA) cytochrome c oxidase subunit I (COI) gene. The COI gene was sequenced showed 99.1-99.8% identity with the EF607565 sequence previously reported. A total of twenty haplotypes were found, and the Korean population showed nineteen haplotypes. Among those, Hap_03 and Hap_08 showed Jeju-do and China-specific COI sequences, respectively. However, Hap_07 had twelve COI sequences from South Korea and records from Hong Kong and Taiwan. Neighbor-joining (NJ) trees constructed from the phylogenetic analyses based on the polymorphisms of the COI haplotypes showed a monophyletic branching pattern within the genus Epinephelus. This indicated that the red spotted grouper populations had evolved from common maternal ancestors. In addition, the Hap_08, which had the COI sequence recorded only from China Sea, was found in the middle of the NJ tree nearby Hap_07 and showed a close relationship with Hap_07. This indicates that Chinese red spotted grouper is also maternally related to other populations in East Asia. Consequently, East Asian red spotted grouper populations are maternally related, as well as sharing the same evolutionary history, and are still affected by the East Asian ocean current (Kuroshio). These findings help to explain the genetic structure and phylogenetic relationship of red spotted grouper and also contribute to research on artificial breeding and industrialization.

• 한국균학회소식:학술대회논문집
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• 2014.05a
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• pp.27-28
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• 2014

Beauveria bassiana (Cordycipitaceae, Hypocreales, Ascomycota) is an anamorphic fungus having a potential to be used as a biological control agent because it parasitizes a wide range of arthropod hosts including termites, aphids, beetles and many other insects. A number of bioactive secondary metabolites (SMs) have been isolated from B. bassiana and functionally verified. Among them, beauvericin and bassianolide are cyclic depsipeptides with antibiotic and insecticidal effects belonging to the enniatin family. Non-ribosomal peptide synthetases (NRPSs) play a crucial role in the synthesis of these secondary metabolites. NRPSs are modularly organized multienzyme complexes in which each module is responsible for the elongation of proteinogenic and non-protein amino acids, as well as carboxyl and hydroxyacids. A minimum of three domains are necessary for one NRPS elongation module: an adenylation (A) domain for substrate recognition and activation; a tholation (T) domain that tethers the growing peptide chain and the incoming aminoacyl unit; and a condensation (C) domain to catalyze peptide bond formation. Some of the optional domains include epimerization (E), heterocyclization (Cy) and oxidation (Ox) domains, which may modify the enzyme-bound precursors or intermediates. In the present study, we analyzed genomes of B. bassiana and its allied species in Hypocreales to verify the distribution of NRPS-encoding genes involving biosynthesis of beauvericin and bassianolide, and to unveil the evolutionary processes of the gene clusters. Initially, we retrieved completely or partially assembled genomic sequences of fungal species belonging to Hypocreales from public databases. SM biosynthesizing genes were predicted from the selected genomes using antiSMASH program. Adenylation (A) domains were extracted from the predicted NRPS, NRPS-like and NRPS-PKS hybrid genes, and used them to construct a phylogenetic tree. Based on the preliminary results of SM biosynthetic gene prediction in B. bassiana, we analyzed the conserved gene orders of beauvericin and bassianolide biosynthetic gene clusters among the hypocrealean fungi. Reciprocal best blast hit (RBH) approach was performed to identify the regions orthologous to the biosynthetic gene cluster in the selected fungal genomes. A clear recombination pattern was recognized in the inferred A-domain tree in which A-domains in the 1st and 2nd modules of beauvericin and bassianolide synthetases were grouped in CYCLO and EAS clades, respectively, suggesting that two modules of each synthetase have evolved independently. In addition, inferred topologies were congruent with the species phylogeny of Cordycipitaceae, indicating that the gene fusion event have occurred before the species divergence. Beauvericin and bassianolide synthetases turned out to possess identical domain organization as C-A-T-C-A-NM-T-T-C. We also predicted precursors of beauvericin and bassianolide synthetases based on the extracted signature residues in A-domain core motifs. The result showed that the A-domains in the 1st module of both synthetases select D-2-hydroxyisovalerate (D-Hiv), while A-domains in the 2nd modules specifically activate L-phenylalanine (Phe) in beauvericin synthetase and leucine (Leu) in bassianolide synthetase. antiSMASH ver. 2.0 predicted 15 genes in the beauvericin biosynthetic gene cluster of the B. bassiana genome dispersed across a total length of approximately 50kb. The beauvericin biosynthetic gene cluster contains beauvericin synthetase as well as kivr gene encoding NADPH-dependent ketoisovalerate reductase which is necessary to convert 2-ketoisovalarate to D-Hiv and a gene encoding a putative Gal4-like transcriptional regulator. Our syntenic comparison showed that species in Cordycipitaceae have almost conserved beauvericin biosynthetic gene cluster although the gene order and direction were sometimes variable. It is intriguing that there is no region orthologous to beauvericin synthetase gene in Cordyceps militaris genome. It is likely that beauvericin synthetase was present in common ancestor of Cordycipitaceae but selective gene loss has occurred in several species including C. militaris. Putative bassianolide biosynthetic gene cluster consisted of 16 genes including bassianolide synthetase, cytochrome P450 monooxygenase, and putative Gal4-like transcriptional regulator genes. Our synteny analysis found that only B. bassiana possessed a bassianolide synthetase gene among the studied fungi. This result is consistent with the groupings in A-domain tree in which bassianolide synthetase gene found in B. bassiana was not grouped with NRPS genes predicted in other species. We hypothesized that bassianolide biosynthesizing cluster genes in B. bassiana are possibly acquired by horizontal gene transfer (HGT) from distantly related fungi. The present study showed that B. bassiana is the only species capable of producing both beauvericin and bassianolide. This property led to B. bassiana infect multiple hosts and to be a potential biological control agent against agricultural pests.

• Asian-Australasian Journal of Animal Sciences
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• v.29 no.5
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• pp.631-639
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• 2016

China has a long history of sheep (Ovis aries [O. aries]) breeding and an abundance of sheep genetic resources. Knowledge of the complete O. aries mitogenome should facilitate the study of the evolutionary history of the species. Therefore, the complete mitogenome of O. aries was sequenced and annotated. In order to characterize the mitogenomes of 3 Chinese sheep breeds (Altay sheep [AL], Shandong large-tailed sheep [SD], and small-tailed Hulun Buir sheep [sHL]), 19 sets of primers were employed to amplify contiguous, overlapping segments of the complete mitochondrial DNA (mtDNA) sequence of each breed. The sizes of the complete mitochondrial genomes of the sHL, AL, and SD breeds were 16,617 bp, 16,613 bp, and 16,613 bp, respectively. The mitochondrial genomes were deposited in the GenBank database with accession numbers KP702285 (AL sheep), KP981378 (SD sheep), and KP981380 (sHL sheep) respectively. The organization of the 3 analyzed sheep mitochondrial genomes was similar, with each consisting of 22 tRNA genes, 2 rRNA genes (12S rRNA and 16S rRNA), 13 protein-coding genes, and 1 control region (D-loop). The NADH dehydrogenase subunit 6 (ND6) and 8 tRNA genes were encoded on the light strand, whereas the rest of the mitochondrial genes were encoded on the heavy strand. The nucleotide skewness of the coding strands of the 3 analyzed mitogenomes was biased toward A and T. We constructed a phylogenetic tree using the complete mitogenomes of each type of sheep to allow us to understand the genetic relationships between Chinese breeds of O. aries and those developed and utilized in other countries. Our findings provide important information regarding the O. aries mitogenome and the evolutionary history of O. aries inside and outside China. In addition, our results provide a foundation for further exploration of the taxonomic status of O. aries.

• Korean Journal of Ichthyology
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• v.18 no.4
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• pp.329-338
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• 2006

Phylogenetic relationships and DNA polymorphism among local populations of the Korean native catfish species, Liobagrus mediadiposalis, have been investigated based on mitochondrial cytochrome b DNA sequences. As a result, three genetically distinct groups of local populations were recognized based on the phylogenetic tree constructed. The first group was called "Nakdong-river group" that included the local populations from Geumho-river, Gyeongho-river, and Deokcheon-river; the second one was "Geum-river group"; the third one was represented as "Seomjin-river group" that included the samples from Seomjin-river, Dongjin-river and Geokum-do. The phylogeny also implied that the ancestral group of L. mediadiposalis have first evolved to Nakdong-river group, and later two local populations (Geum-river and Seomjinriver group) were diverged from the other lineage. DNA polymorphisms we observed were 4.4~4.7% between Geum-river group and Seomjin-river group, 5.1~5.5% between Seomjinriver group and Nakdong-river group, and 5.5~5.7% between Nakdong-river group and Geumriver group. These results indicated the long period of geographic isolation due to the river system in Korea caused such high degrees of DNA polymorphisms between local populations of L. mediadiposalis.

• Journal of KIISE:Computing Practices and Letters
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• v.12 no.2
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• pp.119-128
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• 2006

As dialogue systems are widely required, the research on natural language generation in dialogue has raised attention. Contrary to conventional dialogue systems that reply to the user with a set of predefined answers, a newly developed dialogue system generates them dynamically and trains the answers to support more flexible and customized dialogues with humans. This paper proposes an evolutionary method for generating sentences using interactive genetic programming. Sentence plan trees, which stand for the sentence structures, are adopted as the representation of genetic programming. With interactive evolution process with the user, a set of customized sentence structures is obtained. The proposed method applies to a dialogue-based train booking agent and the usability test demonstrates the usefulness of the proposed method.