• Animal Systematics, Evolution and Diversity
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• v.26 no.3
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• pp.197-201
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• 2010

We sequenced the whole mitochondrial genome of Dendronephthya gigantea (Anthozoa: Octocorallia: Nephteidae), the first mitochondrial genome sequence report in the Family Nephtheidae. The mitochondrial genome of D. gigantea was 18,842 bp in length, and contained 14 protein coding genes (atp6 and 8, cox1-3, cytb, nd1-6 and 4L, and msh1), two ribosomal RNAs, and only one transfer RNA. The gene content and gene order is identical to other octocorals sequenced to date. The portion of the noncoding regions is slightly larger than the other octocorals (5.08% compared to average 3.98%). We expect that the information of gene content, gene order, codon usage, noncoding region and protein coding gene sequence could be used in the further analysis of anthozoan phylogeny.

• Journal of Microbiology and Biotechnology
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• v.22 no.5
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• pp.649-653
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• 2012

A temperate phage was isolated from emetic Bacillus cereus NCTC 11143 by mitomycin C and characterized by transmission electron microscopy and DNA and protein analyses. Whole genome sequencing of Bacillus phage 11143 was performed by GS-FLX. The phage has a dsDNA genome of 39,077 bp and a 35% G+C content. Bioinformatic analysis of the phage genome revealed 49 putative ORFs involved in replication, morphogenesis, DNA packaging, lysogeny, and host lysis. Bacillus phage 11143 could be classified as a member of the Siphoviridae family by morphology and genome structure. Genomic comparisons at the DNA and protein levels revealed homologous genetic modules with patterns and morphogenesis proteins similar to those of other Bacillus phages. Thus, Bacillus phages might have a mosaic genetic relationship.

• Asian-Australasian Journal of Animal Sciences
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• v.27 no.9
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• pp.1219-1227
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• 2014

A whole genome association (WGA) study was carried out to find quantitative trait loci (QTL) for sensory evaluation traits in Hanwoo. Carcass samples of 250 Hanwoo steers were collected from National Agricultural Cooperative Livestock Research Institute, Ansung, Gyeonggi province, Korea, between 2011 and 2012 and genotyped with the Affymetrix Bovine Axiom Array 640K single nucleotide polymorphism (SNP) chip. Among the SNPs in the chip, a total of 322,160 SNPs were chosen after quality control tests. After adjusting for the effects of age, slaughter-year-season, and polygenic effects using genome relationship matrix, the corrected phenotypes for the sensory evaluation measurements were regressed on each SNP using a simple linear regression additive based model. A total of 1,631 SNPs were detected for color, aroma, tenderness, juiciness and palatability at 0.1% comparison-wise level. Among the significant SNPs, the best set of 52 SNP markers were chosen using a forward regression procedure at 0.05 level, among which the sets of 8, 14, 11, 10, and 9 SNPs were determined for the respectively sensory evaluation traits. The sets of significant SNPs explained 18% to 31% of phenotypic variance. Three SNPs were pleiotropic, i.e. AX-26703353 and AX-26742891 that were located at 101 and 110 Mb of BTA6, respectively, influencing tenderness, juiciness and palatability, while AX-18624743 at 3 Mb of BTA10 affected tenderness and palatability. Our results suggest that some QTL for sensory measures are segregating in a Hanwoo steer population. Additional WGA studies on fatty acid and nutritional components as well as the sensory panels are in process to characterize genetic architecture of meat quality and palatability in Hanwoo.

• International Journal of Oral Biology
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• v.45 no.2
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• pp.70-75
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• 2020

The aim of this study was to identify strain KCOM 1265 isolated from subgingival plaque at the species level by comparing 16S ribosomal RNA gene (16S rDNA) and genome sequences. The whole genome of strain KCOM 1265 was extracted using the phenol-chloroform extraction method. 16S rDNA was amplified using polymerase chain reaction and sequenced using the dideoxy chain termination method. Pairwise genome comparison was performed using average nucleotide identity (ANI) and genome-to-genome distance (GGD) analyses. The data showed that the percent similarity of 16S rDNA sequence of strain KCOM 1265 was 99.6% as compared with those of Fusobacterium polymorphum ATCC 10953^T and Fusobacterium hwasookii KCOM 1249^T. The ANI values of strain KCOM 1265 with F. polymorphum ATCC 10953^T and F. hwasookii KCOM 1249^T were 95.8% and 93.0%, respectively. The GGD values of strain KCOM 1265 with F. polymorphum ATCC 10953^T and F. hwasookii KCOM 1249^T were 63.9% and 49.6%, respectively. These results indicate that strain KCOM 1265 belongs to F. polymorphum.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2005.09a
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• pp.3-3
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• 2005

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2002.06b
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• pp.93-107
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• 2002

• Proceedings of the Microbiological Society of Korea Conference
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• 2007.05a
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• pp.143-143
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• 2007

• Proceedings of the Microbiological Society of Korea Conference
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• 2009.05a
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• pp.110-110
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• 2009

• Journal of Microbiology and Biotechnology
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• v.33 no.8
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• pp.1030-1038
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• 2023

Lactiplantibacillus plantarum, previously named Lactobacillus plantarum, is a facultative, homofermentative lactic acid bacterium widely distributed in nature. Several Lpb. plantarum strains have been demonstrated to possess good probiotic properties, and Lpb. plantarum HOM3204 is a potential probiotic strain isolated from homemade pickled cabbage plants. In this study, whole-genome sequencing was performed to acquire genetic information and predict the function of HOM3204, which has a circular chromosome of 3,232,697 bp and two plasmids of 48,573 and 17,060 bp, respectively. Moreover, various oxidative stress-related genes were identified in the strain, and its antioxidant activity was evaluated in vitro and in vivo. Compared to reference strains, the intracellular cell-free extracts of Lpb. plantarum HOM3204 at a dose of 10¹⁰ colony-forming units (CFU)/ml in vitro exhibited stronger antioxidant properties, such as total antioxidant activity, 2,2-diphenyl-1-picrylhydrazyl radical scavenging rate, superoxide dismutase activity, and glutathione (GSH) content. Daily administration of 10⁹ CFU Lpb. plantarum HOM3204 for 45 days significantly improved the antioxidant function by increasing the glutathione peroxidase activity in the whole blood and GSH concentration in the livers of D-galactose-induced aging mice. These results suggest that Lpb. plantarum HOM3204 can potentially be used as a food ingredient with good antioxidant properties.

• The Korean Journal of Malacology
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• v.26 no.4
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• pp.317-326
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• 2010

The availability of fast and inexpensive sequencing technology has enabled researchers around the world to conduct many genome sequencing and expressed sequence tag (EST) projects of diverse organisms. In recent years, whole genome projects have been undertaken to sequence ten species from the phylum Mollusca. These include Aplysia californica, Lottia gigantea, Crassostrea virginica, Spisula solidissima, Mytilus californianus, Biomphalaria glabrata, Crepidula fornicata, Elysia chlorotica, Lottia scutum and Radix balthica. Additionally, complete mitochondrial genomes of 91 mollusks have been reported. In Korea, EST projects have been conducted in nine mollusk species that include Nesiohelix samarangae, Pisidium (Neopisidium) coreanum, Physa acuta, Incilaria fruhstorferi, Meretrix lusoria, Ruditapes philippinarum, Nordotis gigantea, Crassostrea gigas and Laternula elliptica. Finally, the mitochondrial genome projects from the Pacific Oyster (Crassostrea gigas) and the rock shell (Thais clavigera) have been conducted and reported. However, no systemic mollusk genome project has so far been conducted in Korea. In this report, the current status and research trends in mollusk genome study in Korea will be discussed.