• Mycobiology
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• v.50 no.1
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• pp.66-78
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• 2022

The identification of oleaginous yeast species capable of simultaneously utilizing xylose and glucose as substrates to generate value-added biological products is an area of key economic interest. We have previously demonstrated that the Cutaneotrichosporon dermatis NICC30027 yeast strain is capable of simultaneously assimilating both xylose and glucose, resulting in considerable lipid accumulation. However, as no high-quality genome sequencing data or associated annotations for this strain are available at present, it remains challenging to study the metabolic mechanisms underlying this phenotype. Herein, we report a 39,305,439 bp draft genome assembly for C. dermatis NICC30027 comprised of 37 scaffolds, with 60.15% GC content. Within this genome, we identified 524 tRNAs, 142 sRNAs, 53 miRNAs, 28 snRNAs, and eight rRNA clusters. Moreover, repeat sequences totaling 1,032,129 bp in length were identified (2.63% of the genome), as were 14,238 unigenes that were 1,789.35 bp in length on average (64.82% of the genome). The NCBI non-redundant protein sequences (NR) database was employed to successfully annotate 11,795 of these unigenes, while 3,621 and 11,902 were annotated with the Swiss-Prot and TrEMBL databases, respectively. Unigenes were additionally subjected to pathway enrichment analyses using the Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), Cluster of Orthologous Groups of proteins (COG), Clusters of orthologous groups for eukaryotic complete genomes (KOG), and Non-supervised Orthologous Groups (eggNOG) databases. Together, these results provide a foundation for future studies aimed at clarifying the mechanistic basis for the ability of C. dermatis NICC30027 to simultaneously utilize glucose and xylose to synthesize lipids.

• Journal of Mushroom
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• v.19 no.4
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• pp.285-293
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• 2021

The purpose of this study was to identify and characterize the laccase genes of Flammulina velutipes var. lupinicola. Five laccase genes (g1934, g1937, g2415, g2539, g5858) were selected based on the copper binding site and signal peptide analysis results using the laccase gene selected from the F. velutipes var. lupinicola genome. The size of the laccase genes of F. velutipes var. lupinicola were 1,488 bp~1,662 bp. As a result of cDNA sequence analysis, 14 to 17 introns were identified in the laccase genes. The cleavage site predicted as the signal peptide of the laccase gene was found to be located between 20 bp and 34 bp from the N-terminus. In addition, separation and purification were performed to characterize the F. velutipes var. lupinicola laccases, and the optimal activity of the separated and purified proteins were analyzed by pH, temperature and time. Five bands with laccase activity were found from zymogram analysis. The optimal pH of the reaction was 5.5, the optimal temperature was found to be 40℃. Therefore, characterization of the laccase genes identified in this study should help in better understanding the biomass decomposition of F. velutipes var. lupinicola.

• Journal of Life Science
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• v.31 no.7
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• pp.671-676
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• 2021

A cDNA encoding the protein lethal (2) essential for life [l(2)efl] was cloned from Gryllus bimaculatus and named GBl(2)efl. This protein is composed of 189 amino acids, including an N-glycosylation site and 15 phosphorylation sites. Its predicted molecular mass is 21.19 kDa, with a theoretical isoelectric point of 6.2. The secondary structure of GBl(2)efl was predicted from the identification of random coils (56.08%), alpha helices (22.22%), extended strands (17.99%), and beta turns (3.7%) through sequence analyses. A homology analysis revealed that GBl(2)efl exhibited a high similarity with other species at the amino acid level, ranging from 52% to 69%. While GBl(2)efl mRNA expression was higher in the dorsal longitudinal flight muscle following a three-day starvation and in the Malpighian tubules following a one-day starvation, no changes in expression were detected in other tissues. Furthermore, tunicamycin-induced endoplasmic reticulum (ER) stress resulted in an approximately 1.8-fold higher expression in the fat body compared with the wild type.

• Journal of Veterinary Science
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• v.23 no.6
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• pp.12.01-12.10
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• 2022

Background: Staphylococcus aureus and Streptococcus agalactiae are the main cause of clinical mastitis in dairy cattle in Argentina, whereas coagulase-negative staphylococci (CNS) and environmental streptococci are the main cause of subclinical mastitis. Bacteria isolated from infected animals show increasing antimicrobial resistance. Objectives: This study aims to determine the antimicrobial resistance of staphylococci and streptococci isolated from milk with mastitis, and to genotypically characterize the methicillin-resistant (MR) staphylococci. Methods: Isolation was performed on blood agar and identification was based on biochemical reactions. Antimicrobial susceptibility was according to the Clinical and Laboratory Standards Institute guidelines. The antimicrobial resistance genes, SCCmec type and spa type were detected by the polymerase chain reaction method. Results: We isolated a total of 185 staphylococci and 28 streptococci from 148 milk samples. Among the staphylococcal isolates, 154 were identified as CNS and 31 as S. aureus. Among the 154 CNS, 24.6% (n = 38) were resistant to penicillin, 14.9% (n = 23) to erythromycin, 17.5% (n = 27) to clindamycin, 6.5% (n = 10) to cefoxitin and oxacillin. Among the S. aureus isolates, 16.1% (n = 5) were resistant to penicillin, 3.2% (n = 1) to cefoxitin and oxacillin (MRSA). Six MR isolates (5 CNS and 1 MRSA) were positive to the mecA gene, and presented the SCCmec IVa. The MRSA strain presented the sequence type 83 and the spa type 002. Among the 28 streptococcal isolates, 14.3% (n = 4) were resistant to penicillin, 10.7% (n = 3) to erythromycin and 14.3% (n = 4) to clindamycin. Conclusions: The present findings of this study indicate a development of antimicrobial resistance in main bacteria isolated from cows with mastitis in Argentina.

• Research in Plant Disease
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• v.28 no.4
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• pp.231-236
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• 2022

Oxypetalum coeruleum, commonly known as Tweedia, is a perennial herbaceous plant of the Apocynaceae family native to southern Brazil and Uruguay. Tweedia plants are grown as one of the most popular ornamental flowers for floral arrangement in Korea. In May 2021, several tweedia plants in a single greenhouse in Gimje, Jeollabuk-do were found to show virus-like symptoms including necrotic rings, vein-clearing, chlorotic mottle, and mosaic on the leaves, and necrosis on the stems. Here, we have identified tomato spotted wilt virus (TSWV) in symptomatic tweedia leaves by applying high-throughput RNA sequencing. In the result, a single infection by TSWV was verified without mixed infections of different virus species. To confirm the presence of TSWV, a reverse transcription polymerase chain reaction was performed with a specific primer set to the N gene of TSWV. The complete genomic sequence of L, M, and S segments of TSWV 'Oxy' isolate were determined and deposited in GenBank under accession numbers LC671525, LC671638, and LC671639, respectively. In the phylogenetic tree analysis by maximum likelihood method, 'Oxy' isolate showed a high relationship with TSWV 'Gumi' isolate from Gerbera jamesonii in Gyeongsangbuk-do, Korea; for all three RNA segments. To our knowledge, this is the first report of TSWV infection of O. coeruleum in Korea.

• Design Convergence Study
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• v.15 no.5
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• pp.71-83
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• 2016

Interior panels are usually used in finishing of interior walls for not only decorative effects but also information transfer. According to designer's design placing interior panels may need repetitive tasks and the emphasis of this paper is to support an automation of these tasks. Considering the utilization characteristics of interior panels, we propose three method to present patterns by using bitmap image pixels and interior panels' shape changes, based on the theoretical consideration. In addition, in order to approve the possibility of the proposed methods, we have implemented the BIM based interior panels auto layout tool which applied one of the three methods to present patterns by using bitmap image pixel values and panel identification attributes. This tool also supports auto generation of quantity and panel arrangement sequence information that will be used in future construction phase. We expect that this approach will also be used in other decorative objects which require repetition of the basic units, such as floor tiles.

• Journal of Intelligence and Information Systems
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• v.29 no.2
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• pp.323-338
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• 2023

TV advertising with deep analysis of watching pattern of audiences is important to set-top box audience targeting. Applying session-based recommendation model(SBR) to internet commercial, or recommendation based on searching history of user showed its effectiveness in previous studies, but applying SBR to the TV advertising was difficult in South Korea due to data unavailabilities. Also, traditional SBR has limitations for dealing with user preferences, especially in data with user identification information. To tackle with these problems, we first obtain set-top box data from three major broadcasting companies in South Korea(SKB, KT, LGU+) through collaboration with Korea Broadcast Advertising Corporation(KOBACO), and this data contains of watching sequence of 4,847 anonymized users for 6 month respectively. Second, we develop personalized session-based recommendation model to deal with hierarchical data of user-session-item. Experiments conducted on set-top box audience dataset and two other public dataset for validation. In result, our proposed model outperformed baseline model in some criteria.

• The Sea:JOURNAL OF THE KOREAN SOCIETY OF OCEANOGRAPHY
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• v.12 no.2
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• pp.94-101
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• 2007

Analysis of population structure of Oncorhynchus keta, the most abundant salmon in the East Sea of Korea, has not been much carried out despite its importance as a fishery resource in the North Pacific. Currently, molecular methods are being applied to stock identification and a method of using single nucleotide polymorphisms (SNPs) is getting more popular. In this study, we analyzed the 720 bp long sequence of the mtDNA COIII-ND3-ND4L region in order to examine genetic similarity-dissimilarity among the Korea chum salmons of each stream and their relationship with the Japan chum salmons. A total of 152 individuals were analyzed, 108 from 3 locations of Korea and 44 from 2 locations of japan, which resulted in as many as 29 different haplotypes. Pairwise $F_{ST}$ and AMOVA tests of the populations show that there is no significant population-level genetic difference among the chum salmons analyzed ($F_{ST}<0.07$). On the other hand, haplotype relationships among the individuals reveal that approximately 25% of the Korea salmons consist genetic lineages independent of Japan salmons and also that a genetic lineage exists in the Puk river and the Namdae river salmons independent of the Wangpi river salmons of Korea.

• Journal of Life Science
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• v.18 no.8
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• pp.1090-1095
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• 2008

Marbling (intramuscular fat) is an important factor in determining meat quality in Korean beef market. A grain based finishing system for improving marbling leads to inefficient meat production due to an excessive fat production. Identification of intramuscular fat-specific gene might be achieved more targeted meat production through alternative genetic improvement program such as marker assisted selection (MAS). We carried out ddRT-PCR in 12 and 27 month old Hanwoo steers and detected 300 bp PCR product of the inducible cAMP early repressor (ICER) gene, showing highly gene expression in 27 months old. A 1.5 kb sequence was re-sequenced using primer designed base on the Hanwoo EST sequence. We then predicted the open reading frame (ORF) of ICER gene in ORF finder web program. Tissue distribution of ICER gene expression was analysed in eight Hanwoo tissue using realtime PCR analysis. The highest ICER gene expression showed in Small intestine followed by Longissimus dorsi. Interestingly, the ICER gene expressed 2.5 time higher in longissimus dorsi than in same muscle type, Rump. For gene expression analysis in high- and low marbled individuals, we selected 4 and 3 animal based on the muscle crude fat contents (high is 17-32%, low is 6-7% of crude fat contents). The ICER gene expression was analysed using ANOVA model. Marbling (muscle crude fat contents) was affected by ICER gene (P=0.012). Particularly, the ICER gene expression was 4 times higher in high group (n=4) than low group (n=3). Therefore, ICER gene might be a functional candidate gene related to marbling in Hanwoo.

• Journal of Animal Science and Technology
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• v.50 no.6
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• pp.753-762
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• 2008

The primers for RT-PCR and RACE-PCR were designed by aligning the pig genomic sequence and the human complement factor B(CFB) coding sequence(CDS) from the GenBank. Each PCR product was amplified in pig cDNA and sequencing was carried out. The CDS length of pig CFB gene was determined to be 2298 bp. In addition, the pig CDS was more longer than human and mouse orthologs because of insertion and deletion. The identities of porcine nucleotide sequences with those of human and mice were 84% and 80%, and the identities of amino acids were 79% to 77%, respectively. Three complement control protein(CCP) domains, one Von Willebrand factor A(VWFA) domain and a serine protease domain, that are revealed typically in mammals, were found in the pig CFB gene. Based on the CDSs determined, the primers were designed in intron regions for amplification of entire length of exons. In amplification and direct sequencing with genomic DNAs of six pig breeds, three cSNPs(coding single nucleotide polymorphisms) were identified and verified as missense mutations. Using the Multiplex-ARMS method, we genotyped and verified the mutations identified from direct sequencing. To demonstrate recrudescence, we performed both direct sequencing and Multiplex-ARMS with two randomly selected DNA samples. The genotype of each sample exhibited the same results using both methods. Therefore, three cSNPs were identified from pig CFB gene and that can be used for haplotype analysis of the swine leukocyte antigen(SLA) class III region. Moreover, the results indicate that the Multiplex-ARMS method should be powerful for genotyping of genes in the SLA region.