• Clinical and Experimental Pediatrics
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• v.63 no.6
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• pp.195-202
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• 2020

Developments in next-generation sequencing (NGS) techogies have assisted in clarifying the diagnosis and treatment of developmental delay/intellectual disability (DD/ID) via molecular genetic testing. Advances in DNA sequencing technology have not only allowed the evolution of targeted panels but also, and more currently enabled genome-wide analyses to progress from research era to clinical practice. Broad acceptance of accuracy-guided targeted gene panel, whole-exome sequencing (WES), and whole-genome sequencing (WGS) for DD/ID need prospective analyses of the increasing cost-effectiveness versus conventional genetic testing. Choosing the appropriate sequencing method requires individual planning. Data are required to guide best-practice recommendations for genomic testing, regarding various clinical phenotypes in an etiologic approach. Targeted panel testing may be recommended as a firsttier testing approach for children with DD/ID. Family-based trio testing by WES/WGS can be used as a second test for DD/ID in undiagnosed children who previously tested negative on a targeted panel. The role of NGS in molecular diagnostics, treatment, prediction of prognosis will continue to increase further in the coming years. Given the rapid pace of changes in the past 10 years, all medical providers should be aware of the changes in the transformative genetics field.

• Journal of Korean Port Research
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• v.14 no.4
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• pp.419-427
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• 2000

Today travel demand continues to increase with spread of economic zones. Also, urban freeway plays an important role in intra-zone transportations as a major corridor in a big city. However, most of urban freeways experience a severe congestion with the excess of inflowing or outflowing traffic through freeway ramps. The purpose of this study is to identify the traffic characteristics, analyze the relationships between the traffic characteristics and finally construct the speed predictive models on the ramp junctions of urban freeway under the intelligent transportation system(ITS) settings. From the analyses of traffic characteristics following results were obtained: ⅰ) 24 hours average traffic characteristics flow, occupancy, speed under the ITS settings showed about 40%, 38%, 8.8% increase each on urban freeway junctions period when compared with that under the non-ITS settings each other. Free flow speed and traffic flow on the mainline sections of urban freeway under the ITS settings also showed about 20% and 17% increase when compared with that under the non-ITS, respectively. ⅱ) The upstream when compared speed( $S_{u}$)and downstream occupancy( $O_{d}$) were especially shown to have higher explanatory powers on the stable flow ramp junctions, but the upstream speed( $S_{u}$) and downstream flow( $V_{d}$) were especially shown on the unstable flow ramp junctions of urban freeway under the ITS settings.ngs.ngs.

• Genomics & Informatics
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• v.16 no.4
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• pp.36.1-36.3
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• 2018

Next generation sequencing (NGS), a high-throughput DNA sequencing technology, is widely used for molecular biological studies. In NGS, RNA-sequencing (RNA-Seq), which is a short-read massively parallel sequencing, is a major quantitative transcriptome tool for different transcriptome studies. To utilize the RNA-Seq data, various quantification and analysis methods have been developed to solve specific research goals, including identification of differentially expressed genes and detection of novel transcripts. Because of the accumulation of RNA-Seq data in the public databases, there is a demand for integrative analysis. However, the available RNA-Seq data are stored in different formats such as read count, transcripts per million, and fragments per kilobase million. This hinders the integrative analysis of the RNA-Seq data. To solve this problem, we have developed a web-based application using Shiny, COEX-seq (Convert a Variety of Measurements of Gene Expression in RNA-Seq) that easily converts data in a variety of measurement formats of gene expression used in most bioinformatic tools for RNA-Seq. It provides a workflow that includes loading data set, selecting measurement formats of gene expression, and identifying gene names. COEX-seq is freely available for academic purposes and can be run on Windows, Mac OS, and Linux operating systems. Source code, sample data sets, and supplementary documentation are available as well.

• Microbiology and Biotechnology Letters
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• v.49 no.3
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• pp.440-448
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• 2021

Helicobacter pylori (H. pylori) establishes long-term infections associated with severe gastric diseases such as peptic ulceration and gastric cancer. Exposure to an antibacterial agent can help regulate the expression levels of its pathogenic genes. In this study, we analyzed the transcriptional changes in H. pylori genes induced by β-caryophyllene. We used next-generation sequencing (NGS) to analyze RNA expression changes, and reverse transcription-polymerase chain reaction (RT-PCR) was performed as required to verify the results. The NGS results showed that 30 out of 1,632 genes were expressed differentially by β-caryophyllene treatment. Eleven genes associated with DNA replication, virulence factors, and T4SS components were significantly downregulated. RT-PCR confirmed that treatment reduced the expression levels of 11 genes. RT-PCR showed the reduced expression of 11 genes (dnaE, dnaN, holB, gyrA, cagA, vacA, secA, flgE, virB2, virB4, and virB8) following β-caryophyllene treatment. These results suggest that β-caryophyllene can modulate various H. pylori pathogenic determinants and be a potential therapeutic agent for H. pylori infection.

• Journal of Microbiology and Biotechnology
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• v.32 no.3
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• pp.341-347
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• 2022

In this study, the bacterial community of galchi-baechu kimchi was determined using culture-based and culture-independent techniques (next generation sequencing:NGS), and showed discrepancies between results. Weissella koreensis and Pediococcus inopinatus were the dominant species according to the NGS results, while Bacillus species and P. inopinatus were dominant in the culture-dependent analysis. To identify safe starter candidates, sixty-five Bacillus strains isolated from galchi-baechu kimchi using culture-dependent methods were evaluated for their antibiotic resistance, presence of toxin genes, and hemolytic activity. Strains were then assessed for salt tolerance and protease and lipase activity. As a result, four strains-B. safensis GN5_10, B. subtilis GN5_19, B. velezensis GN5_25, and B. velezensis GT8-were selected as safe starter candidates for use in fermented foods.

• Journal of Life Science
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• v.30 no.1
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• pp.64-69
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• 2020

The European honeybee (Apis mellifera L.) has multiple anti-microbial peptides, but many were unknown and demands for their characterization have increased. This study therefore focused on identifying novel anti-microbial peptides (AMPs) from A. mellifera L. To obtain high-throughput transcriptome data of the honeybee, we implemented next-generation sequencing (NGS), isolating novel AMPs from total RNA, and generated 15,314 peptide sequences, including 44 known, using Illumina HiSeq 2500 technology. The uncharacterized peptides were identified based on specific features of possible AMPs predicted in the sequencing analysis. AMP5, one such uncharacterized peptide, was expressed in the epidermis, body fat, and venom gland of the honeybee. We chemically synthesized this peptide and tested its anti-bacterial activity against Gram-negative Escherichia coli (KACC 10005) and Gram-positive Bacillus thuringiensis (KACC 10168) by anti-microbial assay. AMP5 exhibited anti-bacterial activity against E. coli (MIC50=22.04±0.66 μM) but not against B. thuringiensis. When worker bees were injected with E. coli, AMP5 was up-regulated in the body fat. This study therefore identified AMP5 in adult European honeybees and confirmed its anti-bacterial activity against Gram-negative E. coli.

• Journal of Plant Biotechnology
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• v.42 no.4
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• pp.290-297
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• 2015

Based on the place of its origin, pear tree (Pyrus spp.) is largely divided into European pears (P. communis, cultivated mainly in Europe and the U.S.) and Asian pears (P. pyrifolia, P. bretschneideri, and P. ussuriensis, distributed and grown in East Asian countries including China, Japan, and Korea). Most pear trees have 17 chromosomes (diploidy, 2n=2x=34). Their genetic studies and precise cultivar breeding are highly restricted by conditions such as self-incompatibility controlled by S-locus and juvenility as one major character of fruit crops. Genetic studies on Pyrus have been promoted by the development of various molecular markers. These markers are being utilized actively in various genetic studies, including genetic relationship analysis, genetic mapping, and QTL analysis. In addition, research on pear genetic linkage maps has been extended to studies for the identification of QTL for target traits such as disease resistance and genetic loci of useful traits. NGS technology has radically reduced sequencing expenses based on massive parallel reactions to enable high-capacity and high-efficiency. NGS based genome analyses have been completed for Chinese pear 'Danshansuli' and European pear 'Bartlett'. In Korea, GWAS for agricultural valuable traits such as floral structure, ripening, and total soluble contents have been conducted through resequencing. GBS has been performed for 'Whangkeumbae', 'Cheongsilri', and 'Minibae'.

• Proceedings of the Korean Institute of Information and Commucation Sciences Conference
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• 2015.05a
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• pp.768-770
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• 2015

We performed integration and standardization of the omics data related agriculture. To do this, we requires progressed computational methods and bioinformatics infrastructures for integration, standardization, mining, and analysis. It makes easier biological knowledge to find. we potentialize registration a row and processed data in NABIC (National Agricultural Biotechnology Information Center) and its processed analysis results were offered related researchers. And we also provided various analysis pipelines, NGS analysis (Reference assembly, RNA-seq), GWAS, Microbial community analysis. In addition, the our system was carried out based on the design and build the quality assurance in management omics information system and constructed the infrastructure for utilization of omics analyze system. We carried out major improvement quality of omics information system. First is Improvement quality of registration category for omics based information. Second is data processing and development platform for web UI about related omics data. Third is development of proprietary management information for omics registration database. Forth is management and development of the statistics module producers about omics data. Last is Improvement the standard upload/ download module for Large omics Registration information.

• Current Optics and Photonics
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• v.2 no.3
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• pp.269-279
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• 2018

We are currently investigating the feasibility of a 1.6 m telescope with a laser-guide star adaptive optics (AO) system. The telescope, if successfully commissioned, would be the first dedicated adaptive optics observatory in South Korea. The 1.6 m telescope is an f/13.6 Cassegrain telescope with a focal length of 21.7 m. This paper first reviews atmospheric seeing conditions measured over a year in 2014~2015 at the Bohyun Observatory, South Korea, which corresponds to an area from 11.6 to 21.6 cm within 95% probability with regard to the Fried parameter of 880 nm at a telescope pupil plane. We then derive principal seeing conditions such as the Fried parameter and Greenwood frequency for eight astronomical spectral bands (V/R/I/J/H/K/L/M centered at 0.55, 0.64, 0.79, 1.22, 1.65, 2.20, 3.55, and $4.77{\mu}m$). Then we propose an AO system with a laser guide star for the 1.6 m telescope based on the seeing conditions. The proposed AO system consists of a fast tip/tilt secondary mirror, a $17{\times}17$ deformable mirror, a $16{\times}16$ Shack-Hartmann sensor, and a sodium laser guide star (589.2 nm). The high order AO system is close-looped with 2 KHz sampling frequency while the tip/tilt mirror is independently close-looped with 63 Hz sampling frequency. The AO system has three operational concepts: 1) bright target observation with its own wavefront sensing, 2) less bright star observation with wavefront sensing from another bright natural guide star (NGS), and 3) faint target observation with tip/tilt sensing from a bright natural guide star and wavefront sensing from a laser guide star. We name these three concepts 'None', 'NGS only', and 'LGS + NGS', respectively. Following a thorough investigation into the error sources of the AO system, we predict the root mean square (RMS) wavefront error of the system and its corresponding Strehl ratio over nine analysis cases over the worst ($2{\sigma}$) seeing conditions. From the analysis, we expect Strehl ratio >0.3 in most seeing conditions with guide stars.

• Journal of the Korean Society for Environmental Technology
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• v.19 no.6
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• pp.550-555
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• 2018

International Maritime Organization (IMO) is one of the most effective organizations in evolving international law for the protection and conservation of the marine environment. The IMO, MARPOL(Marine Pollution) 73/78 contains six Annexes that provide an overarching framework for the objectives of the international marine pollution. Annex IV was regulated by 64 th resolution in 2012 to control sea pollution from sewage. In 2014 large-scale wastewater treatment and nutrient removal device was developed with a grant from the Ministry of Oceans and Fisheries. A combined new process of Sequence Batch Reactor (SBR) and Membrane Bioreactor(MBR) was developed to overcome the pollution caused by shipboard sewage. In the present study, shipboard sewage wastewater was treated by mixing and aeration cycle in the newly developed SBR process. Furthermore, during analysis by NGS technique(Macrogen Co., Ltd.), dominant species of bacteria were found in the aeration tank of the Bench-scale wastewater treatment facility. Bacteroidetes and Gammaproteobacteria accounted for 27.1 % of the aerobicbacteria and 16.8 % of the anaerobicbacteria, respectively. Microorganisms play a vital role in shipboard wastewater treatment. A further detailed study is required to understand the precise role of the microorganisms in the wastewater treatment.