• Journal of Life Science
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• v.25 no.3
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• pp.357-367
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• 2015

With the ongoing development of next-generation sequencing (NGS) platforms and advancements in the latest bioinformatics tools at an unprecedented pace, the ultimate goal of sequencing the human genome for less than $1,000 can be feasible in the near future. The rapid technological advances in NGS have brought about increasing demands for statistical methods and bioinformatics tools for the analysis and management of NGS data. Even in the early stages of the commercial availability of NGS platforms, a large number of applications or tools already existed for analyzing, interpreting, and visualizing NGS data. However, the availability of this plethora of NGS data presents a significant challenge for storage, analyses, and data management. Intrinsically, the analysis of NGS data includes the alignment of sequence reads to a reference, base-calling, and/or polymorphism detection, de novo assembly from paired or unpaired reads, structural variant detection, and genome browsing. While the NGS technologies have allowed a massive increase in available raw sequence data, a number of new informatics challenges and difficulties must be addressed to improve the current state and fulfill the promise of genome research. This review aims to provide an overview of major NGS technologies and bioinformatics tools for NGS data analyses.

• Korean Journal of Microbiology
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• v.46 no.2
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• pp.162-168
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• 2010

The sequence diversity of mcyA gene involved in synthesis of microcystins was analyzed in Microcystis spp. isolated from the Korean reservoirs and in the environmental samples taken from the Daechung, Chungju, Yongdam, Soyang, and Euam Reservoirs at the cyanobacterial blooming season. It was estimated that the sequences of mcyA gene in the isolated Microcystis spp. were much conserved when compared with those in GenBank database. A few kinds of clones were dominant in the investigated environmental samples, occupying 87 to 100% of total clones. No mcyA sequences originated from Anabaena spp. or Planktothrix spp. was found. These results indicated that microcystins are produced mainly by Microcystis spp. and the sequences of mcyA genes are much conserved in the investigated Korean reservoirs.

• Journal of the Korean Society of Propulsion Engineers
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• v.17 no.5
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• pp.121-131
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• 2013

The characteristics of flame dynamics occurring near the bluff body was experimentally investigated in a model combustor with V-gutter bluff body. Measurements of chemiluminescence with high speed camera and PIV were performed for visualization of flame structure. Flashback occurs due to the change of pressure gradient in the combustor, and the flashback distance depends on equivalent ratio. Unstable flames can be classified into three types depending on the flashback distance and structure. When the flame goes over the bluff body, an unusual flame structure occurs at the front of the bluff body. Re-stabilization takes place as the flame moves downstream of the combustor. This process is supported by a strong vortex structure behind the bluff body.

• Korean Journal of Microbiology
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• v.45 no.4
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• pp.430-434
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• 2009

Bacterial 16S rRNA gene sequences have been widely used for the studies on molecular phylogeny, evolutional history, and molecular detections. Bacterial genomes have multiple rRNA operons, of which gene sequences sometimes are variable. In the present study, heterogeneity of the Vibrio 16S rRNA gene sequences were investigated. Vibrio 16S rRNA sequences were obtained from GenBank databases, considering the completion of gene annotation of Vibrio genome sequences. These included V. cholerae, V. harveyi, V. parahaemolyticus, V. splendidus, and V. vulnificus. Chromosome 1 of the studied Vibrio had 7~10 copies of the 16S rRNA gene, and their intragenomic variations were less than 0.9% dissimilarity (more than 99.1% DNA similarity). Chromosome 2 had none or single 16S rRNA gene. Intragenomic 16S rRNA genotypes were detected at least 5 types (V. vulnificus #CMCP6) to 8 types (V. parahaemolyticus #RIMD 2210633, V. harveyi #ATCC BAA-1116). These suggest that Vibrio has high heterogeneity of the 16S rRNA gene sequences.

• Journal of the Korean Society of Propulsion Engineers
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• v.24 no.5
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• pp.13-20
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• 2020

The effect of the relative distance between two cavity flame holders on the performance of a supersonic combustor was experimentally investigated. A rectangular cross-sectional combustor model with one cavity flame holder on each of two facing walls was used, with two difference distances between cavities of 135 mm and 220 mm. The fuel equivalence ratio was varied as 0.16 and 0.38. A direct-connected type test facility was used to provide Mach 2 flow condition. The test results revealed that the combustion pressure was higher for the shorter cavity distance case. But fuel equivalence ratio did not have large effect on the combustion pressure. It was concluded that, to get higher combustor pressure, there needs to be further combustor configuration change such as smaller cavity distance or tandem cavity installation.

• The Journal of the Korea Contents Association
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• v.22 no.2
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• pp.762-769
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• 2022

Genetic testing in prenatal diagnosis is a precious tool providing valuable information in clinical management and parental decision-making. For the last year, cytogenetic testing methods, such as G-banding karyotype analysis, fluorescent in situ hybridization, chromosomal microarray, and gene panels have evolved to become part of routine laboratory testing. However, the limitations of each of these methods demonstrate the need for a revolutionary technology that can alleviate the need for multiple technologies. The recent introduction of new genomic technologies based on next-generation sequencing has changed the current practice of prenatal testing. The promise of these innovations lies in the fast and cost-effective generation of genome-scale sequence data with exquisite resolution and accuracy for prenatal diagnosis. Here, we review the current state of sequencing-based pediatric diagnostics, associated challenges, as well as future prospects.

• The Journal of the Petrological Society of Korea
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• v.19 no.3
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• pp.209-225
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• 2010

The Shinri area near the Yedang Lake, the eastern part of the Hongseong area in SW Gyeonggi Massif, consists of the Neoproterozoic Duckjeongri granodiorite-tonalite, mylonitized amphibole-bearing orthogneiss and impure marble with lens-shaped garnet-bearing metabasites. In this paper, we report mineralogical and geochemical data of Neoproterozoic lens-shaped garnet-bearing metabasites within marble of the Shinri area. The $SiO_2$ contents of garnet-bearing metabasites in marble vary between ~46.98 and 51.17 wt%, and the $Na_2O$ + $K_2O$ contents fall between ~1.95 and 2.85 wt%, similar to the tholeiitic sub-alkaline basaltic rocks. In the Zr/Y vs. Zr diagram, garnet-bearing metabasites also plot in the subalkaline basaltic rocks. The chondrite-normalized REE patterns for Shinri garnet-bearing metabasites show relatively flat patterns to that of chondrite. They show slight LREE-enriched and depleted patterns. The major and trace element data from lens-shaped garnet-bearing metabasites in marble of the Shinri area suggest that these rocks were formed in within plate. In contrast, previous major and trace element data of high pressure type garnet-bearing metabasites from the mafic-ultramafic complex in the Baekdong and Bibong areas suggest that these rocks were formed in a nascent arc to backarc spreading center within subduction zone setting. Based on mineral assemblage and mineral chemistry, P-T estimates for Shinri garnet-bearing metabasites are 9.6-12.7 kb, $695-840^{\circ}C$ for inclusions in the core, and 9.6-13.6 kb, $630-755^{\circ}C$ for those in the rim. These P-T estimates are distinct from those of the Baekdong and Bibong garnet-bearing metabasites with isothermal decompressional retrograde P-T path. In addition to Triassic tectonic activity previously reported in the Shinri area of Hongseong, the details of metamorphic history such as protolith age and Neo-Proterozoic metamorphic episode need to be solved.

• Reproductive and Developmental Biology
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• v.29 no.1
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• pp.9-13
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• 2005

This study was performed to analyze the sequence variation in mtDNA D-loop and their effects on milk and milk fat production in Holstein cows. The analyzed sequences were compared with previously published sequences from other cattle breeds (GenBank J01394). PCR was performed to amplify a total of 964 bp between nucleotide 15758 and 383 within D-loop region of mtDNA using specific primers. Thirty five polymorphic sites by nucleotide substitution were found in mtDNA. The frequencies of positions at 106, 169, 16057, 16231 and 16255 nt with high levels of sequence polymorphism were 0.090, 0.555, 0.055, 0.090 and 0.050, respectively. The substitution effect at 169 nt was found significant on milk production, and substitution effect at 16118, 16139 and 16302 nt was highly significant (p<0.1) on milk fat production. Polymorphism of mtDNA sequence in D-loop region might be useful for the analysis of cytoplasmic genetic variation and associations with the other economically important traits and maternal lineage analysis in Holstein cows.

• Korean Journal of Medicinal Crop Science
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• v.16 no.1
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• pp.20-26
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• 2008

Anemarrhena asphodeloides (Korean name "Ji-Mo") has been used for oriental medicinal purposes in Korea, China and Japan. In this study, 29 A. asphodeloides samples were collected including 3 certified A. asphodeloides plants and many commercially marketed A. asphodeloides products. Chloroplast trnL-F regions of the "Ji-Mo" samples were sequenced and used to identify whether the samples were genuine A. asphodeloides or not. As the result, the trnL-F sequences of all the "Ji-Mo" samples were shown to be identical and it was proven that commercially available medicinal products "Ji-Mo" are genuine A. asphodeloides. Phylogenetic tree of. A. asphodeloides using the trnL-F sequences was constructed and compared with phylogenetic tree using rubisco large subunit (rbcL) gene sequences. In these tree, A. asphodeloides was affiliated in the family Agavaceae in the order Asparagales. It is proven that trnL-F phylogenetic tree is useful to study taxonomic position of A. asphodeloides.

• Korean Journal of Ichthyology
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• v.25 no.3
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• pp.149-156
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• 2013

Phylogenetic relationships and DNA polymorphism among local populations of two Korean gobiidae species: Boleophthalmus pectinirostris and Scartelaos gigas were investigated based on 12S and 16S mitochondrial DNA and mitochondrial cytochrome b DNA sequences. DNA polymorphisms of B. pectinirostris between Suncheon and Gunsan populations were 100% identity from 434 bp segment of 12S rRNA gene and from 444 bp segment of mitochondrial cytochrome b genes, and 99.6% (2 bp different) identity from 484 bp segments of 16S rRNA genes. These results indicated the long period of geographic isolation between two populations of B. pectinirostris in Korea caused such high degrees of DNA polymorphisms. Based on the phylogenetic tree constructed from the two gobiid species in Korea, two genetically distinct groups of B. pectinirostris and S. gigas groups were recognized.