• Journal of Microbiology and Biotechnology
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• v.27 no.9
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• pp.1670-1680
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• 2017

Lignocellulose, composed mostly of cellulose, hemicellulose, and lignin generated through secondary growth of woody plant, is considered as promising resources for biofuel. In order to use lignocellulose as a biofuel, biodegradation besides high-cost chemical treatments were applied, but knowledge on the decomposition of lignocellulose occurring in a natural environment is insufficient. We analyzed the 16S rRNA gene and metagenome to understand how the lignocellulose is decomposed naturally in decayed Torreya nucifera (L) of Bija forest (Bijarim) in Gotjawal, an ecologically distinct environment. A total of 464,360 reads were obtained from 16S rRNA gene sequencing, representing diverse phyla; Proteobacteria (51%), Bacteroidetes (11%) and Actinobacteria (10%). The metagenome analysis using single molecules real-time sequencing revealed that the assembled contigs determined originated from Proteobacteria (58%) and Actinobacteria (10.3%). Carbohydrate Active enZYmes (CAZy)- and Protein families (Pfam)-based analysis showed that Proteobacteria was involved in degrading whole lignocellulose, and Actinobacteria played a role only in a part of hemicellulose degradation. Combining these results, it suggested that Proteobacteria and Actinobacteria had selective biodegradation potential for different lignocellulose substrates. Thus, it is considered that understanding of the systemic microbial degradation pathways may be a useful strategy for recycle of lignocellulosic biomass, and the microbial enzymes in Bija forest can be useful natural resources in industrial processes.

• Korean Journal of Microbiology
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• v.54 no.1
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• pp.77-78
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• 2018

Staphylococcus aureus is a Gram-positive and a round-shaped bacterium of Firmicutes phylum, and is a common cause of skin infections, respiratory infections, and food poisoning. Bacteriophages infecting S. aureus can be an effective treatment for S. aureus infections. Here, the draft genomic sequence is announced for a lytic bacteriophage SA7 infecting S. aureus isolates. The bacteriophage SA7 was isolated from a sewage water sample near a livestock farm in Chungcheongnam-do, South Korea. SA7 has a genome of 34,730 bp and 34.1% G + C content. The genome has 53 protein-coding genes, 23 of which have predicted functions from BLASTp analysis, leaving the others conserved proteins with unknown function.

• Journal of the Korean Society for Railway
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• v.15 no.3
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• pp.300-305
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• 2012

The saving of time, which is defined as the demand from passengers and the supply from the urban railway, must be balanced. The selected factors influencing on the balance are the traffic, customer contact facilities, the number of failures, customer complaints(VOC), passenger moving time and transfer stations. Also, the overall ratio of SMRT's 4 lines is generated by differentiating the rate of each attribute in each factor. This is not only to differentiate the stations with peculiar factors but also to standardize criteria of the personalized services. Furthermore, as part of standardization, standard drawings of facility management are prepared for the improvement on the management of human resource and material. The drawings include passenger moving lines, location of safety incidents and also indicate the rating of the factors in each station and overall evaluation rating. In conclusion, this thesis aims to improve customer satisfaction constantly by reducing passenger moving time, through the differentiated management of each station.

• Journal of the Korea Society of Computer and Information
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• v.26 no.11
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• pp.247-254
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• 2021

In this paper, we propose antecedent factors that influence the Information Literacy Competency of female farmers using smart devices. The study was analyzed using the materials from the "Primary Survey of Information Literacy Competency Measurement Index for Female Farmers" by the Rural Development Administration. The target of the survey was 200 women working on the farms. The descriptive, correlation, and multiple regression analyses, t-test, and ANOVA using SPSS 21.0 program were performed. Study results found that among the psychological factors, Self-efficacy and Innovativeness have positive effects on Information Literacy Competency. Among the Sociodemographic factors, the education level, presence of smartpads, and tiem spent on smartphones have positive effects on Information Literacy Competency. Findings of the results contributed to the understanding of the Information Literacy Competency for female farmers, who have lack of infromarion on smrt devices, and suggested the direction of enhancing the level of Information Literacy Competency for female farmers.

• Journal of Microbiology and Biotechnology
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• v.29 no.5
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• pp.794-808
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• 2019

Bacillus velezensis strain WRN014 was isolated from banana fields in Hainan, China. Bacillus velezensis is an important member of the plant growth-promoting rhizobacteria (PGPR) which can enhance plant growth and control soil-borne disease. The complete genome of Bacillus velezensis WRN014 was sequenced by combining Illumina Hiseq 2500 system and Pacific Biosciences SMRT high-throughput sequencing technologies. Then, the genome of Bacillus velezensis WRN014, together with 45 other completed genome sequences of the Bacillus velezensis strains, were comparatively studied. The genome of Bacillus velezensis WRN014 was 4,063,541bp in length and contained 4,062 coding sequences, 9 genomic islands and 13 gene clusters. The results of comparative genomic analysis provide evidence that (i) The 46 Bacillus velezensis strains formed 2 obviously closely related clades in phylogenetic trees. (ii) The pangenome in this study is open and is increasing with the addition of new sequenced genomes. (iii) Analysis of single nucleotide polymorphisms (SNPs) revealed local diversification of the 46 Bacillus velezensis genomes. Surprisingly, SNPs were not evenly distributed throughout the whole genome. (iv) Analysis of gene clusters revealed that rich gene clusters spread over Bacillus velezensis strains and some gene clusters are conserved in different strains. This study reveals that the strain WRN014 and other Bacillus velezensis strains have potential to be used as PGPR and biopesticide.

• Journal of Animal Science and Technology
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• v.63 no.6
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• pp.1411-1422
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• 2021

Lactobacillus acidophilus is a gram-positive, microaerophilic, and acidophilic bacterial species. L. acidophilus strains in the gastrointestinal tracts of humans and other animals have been profiled, but strains found in the canine gut have not been studied yet. Our study helps in understanding the genetic features of the L. acidophilus C5 strain found in the canine gut, determining its adaptive features evolved to survive in the canine gut environment, and in elucidating its probiotic functions. To examine the canine L. acidophilus C5 genome, we isolated the C5 strain from a Korean dog and sequenced it using PacBio SMRT sequencing technology. A comparative genomic approach was used to assess genetic relationships between C5 and six other strains and study the distinguishing features related to different hosts. We found that most genes in the C5 strain were related to carbohydrate transport and metabolism. The pan-genome of seven L. acidophilus strains contained 2,254 gene families, and the core genome contained 1,726 gene families. The phylogenetic tree of the core genes in the canine L. acidophilus C5 strain was very close to that of two strains (DSM20079 and NCFM) from humans. We identified 30 evolutionarily accelerated genes in the L. acidophilus C5 strain in the ratio of non-synonymous to synonymous substitutions (dN/dS) analysis. Five of these thirty genes were associated with carbohydrate transport and metabolism. This study provides insights into genetic features and adaptations of the L. acidophilus C5 strain to survive the canine intestinal environment. It also suggests that the evolution of the L. acidophilus genome is closely related to the host's evolutionary adaptation process.

• Proceedings of the Korean Society of Crop Science Conference
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• 2022.10a
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• pp.28-28
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• 2022

This paper presents the first genome assemblies of Philippine mangoes that provide valuable reference for varietal improvement and genomic studies on mango and related fruit crops. WE sequenced whole genomes of3 species, Mangifera odorata (Huani), Mangifera altissima (Paho), and Mangifera indica 'Carabao' (Sweet Elena). 'Carabao' is the major export variety of the Philippines; Paho is identified as vulnerable by the IUCN Red List of Threatened Species; Huani has fruit sap acrid which is the primary defense mechanism against insects and birds. We used Falcon, a diploid aware -de novo assembler to assemble SMRT generated long-read sequences. Falcon-unzip was employed to phase the output assembly producing larger contig sets (primary contigs) and shorter contigs corresponding to haplotypes (haplotigs). Assembly statistics were generated by comparing the assembly to a reference genome, Tommy Atkins, using Quality Assessment Tool (QUAST). Moreover, the extent of duplication and completeness of gene content was measured using Benchmarking Universal Single-Copy Orthologs (BUSCO). Draft assemblies with high duplications were processed using Purge Haplotigs and Purge Dups to lessen duplications with minimal impact on genome completeness. De novo assemblies of Huani, Paho and 'Carabao' were then generated with primary contig sizes of 463.64 Mb, 508.95 Mb and 401.51 Mb respectively. These draft assemblies of Huani, Paho and 'Carabao' showed 96.90%, 95.17% and 99.07% complete BUSCOs respectively which is comparable to 'Tommy Atkins' genome (98.6%). Using two mango transcriptome data (pooled RNA-seq from different mango varieties and tissues), 91-96% or 24-30 million reads were successfully mapped back for each generated assembly indicating high degree of completeness. The results obtained demonstrated the highly contiguous, phased, and near complete genome assembly of three Philippine mango species for structural and functional annotation of gene units, especially those with economic importance.

• The Journal of Korean Society for Radiation Therapy
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• v.29 no.2
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• pp.9-17
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• 2017

Purpose: The tissue description and electron density indicated by the Computed Tomography(CT) number (also known as Hounsfield Unit) in radiotherapy are important in ensuring the accuracy of CT-based computerized radiotherapy planning. The internal metal implants, however, not only reduce the accuracy of CT number but also introduce uncertainty into tissue description, leading to development of many clinical algorithms for reducing metal artifacts. The purpose of this study was, therefore, to investigate the accuracy and the clinical applicability by analyzing date from SMART MAR (GE) used in our institution. Methode: and material: For assessment of images, the original images were obtained after forming ROIs with identical volumes by using CIRS ED phantom and inserting rods of six tissues and then non-SMART MAR and SMART MAR images were obtained and compared in terms of CT number and SD value. For determination of the difference in dose by the changes in CT number due to metal artifacts, the original images were obtained by forming PTV at two sites of CIRS ED phantom CT images with Computerized Treatment Planning (CTP system), the identical treatment plans were established for non-SMART MAR and SMART MAR images by obtaining unilateral and bilateral titanium insertion images, and mean doses, Homogeneity Index(HI), and Conformity Index(CI) for both PTVs were compared. The absorbed doses at both sites were measured by calculating the dose conversion constant (cCy/nC) from ylinder acrylic phantom, 0.125cc ionchamber, and electrometer and obtaining non-SMART MAR and SMART MAR images from images resulting from insertions of unilateral and bilateral titanium rods, and compared with point doses from CTP. Result: The results of image assessment showed that the CT number of SMART MAR images compared to those of non-SMART MAR images were more close to those of original images, and the SD decreased more in SMART compared to non-SMART ones. The results of dose determinations showed that the mean doses, HI and CI of non-SMART MAR images compared to those of SMART MAR images were more close to those of original images, however the differences did not reach statistical significance. The results of absorbed dose measurement showed that the difference between actual absorbed dose and point dose on CTP in absorbed dose were 2.69 and 3.63 % in non-SMRT MAR images, however decreased to 0.56 and 0.68 %, respectively in SMART MAR images. Conclusion: The application of SMART MAR in CT images from patients with metal implants improved quality of images, being demonstrated by improvement in accuracy of CT number and decrease in SD, therefore it is considered that this method is useful in dose calculation and forming contour between tumor and normal tissues.