• Journal of Life Science
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• v.31 no.4
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• pp.410-417
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• 2021

Next-generation sequencing (NGS) is a high-throughput technique for sequencing large numbers of DNA fragments that are prepared from a genome. This sequencing technique has been used to elucidate whole genome sequences of living organisms and to analyze complementary DNA (cDNA) or chromatin immunoprecipitated DNA (ChIPed DNA) at the genome level. After NGS, the use of proper tools is important for processing and analyzing data with reasonable parameters. However, handling large-scale sequencing data and programing for data analysis can be difficult. The Galaxy platform, a public web service system, provides many different tools for NGS data analysis, and it allows researchers to analyze their data on a web browser with no deep knowledge about bioinformatics and/or programing. In this study, we explain the procedure for preparing chromatin immunoprecipitation-sequencing (ChIP-seq) libraries and steps for analyzing ChIP-seq data using the Galaxy platform. The data analysis steps include the NGS data upload to Galaxy, quality check of the NGS data, premapping processes, read mapping, the post-mapping process, peak-calling and visualization by window view, heatmaps, average profile, and correlation analysis. Analysis of our histone H3K4me1 ChIP-seq data in K562 cells shows that it correlates with public data. Thus, NGS data analysis using the Galaxy platform can provide an easy approach to bioinformatics.

• Journal of Life Science
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• v.16 no.7 s.80
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• pp.1112-1118
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• 2006

Bordetella bronchiseptica, the agent of swine atrophic rhinitis and kennel cough in dogs, is a mucosal pathogen and produces the hydroxamate type alcaligin siderophore under iron-limited conditions. Genes involved in alcaligin siderophore biosynthesis are contained in an alcABCDE operon. In order to provide direct evidence for the role of AlcA in alcaligin biosynthesis, we needed a B. bronchiseptica mutant carrying alcA gene deletion. A 0.6 kb alcA 5'-flanking and 0.7kb 3'-flanking DNA fragments were PCR amplified with the use of pCP1.11 as a template DNA. The 5'-and 3'-flanking DNA fragments were joined in a suicide plasmid, resulting in a recombinant suicide plasmid pDM1. After introduction of pDM1 into B. bronchiseptica by conjugation, the allelic exchange technique was performed and a B. bronchiseptica alcA deletion mutant, named B. bronchiseptica H1, was obtained. The mutant strain produced reduced amount of siderophore as expected. When a plasmid containing complete alcA gene was transformed back into the mutant, the complemented mutant recovered ability of siderophore production. These results indicated that AlcA is one of essential components for the alcaligin siderophore biosynthesis. The mutant strains obtained in this study will be used in the further studies for the biochemical function of AlcA.

• Proceedings of the Korean Society of Sericultural Science Conference
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• 2003.04a
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• pp.68-68
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• 2003

The glutathione-S-transferases (GSTs) are enzymes responsible for the protection of cells from chemical toxicants and oxidative stress. In insects, GSTs have been particularly known to be implicated in the resistance to insecticides. In this study, a cDNA encoding the GST gene homologue was isolated from the cDNA library of the mole cricket, Gryllotalpa orientalis. (omitted)

• Journal of Species Research
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• v.9 no.3
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• pp.181-190
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• 2020

Monoraphidium subclavatum (FBCC-A409) of this study clustered in the same clade as Messastrum gracile strains in the 18S rDNA phylogeny. Compared to Messastrum gracile, Monoraphidium subclavatum did not form a colony, and the curvature of the cell was slightly curved or slightly crescent-shaped. This result means that the genus Monoraphidium is still based on the morphospecies concept, and was not monophyletic and not distinguishable as a separate genus. Two Stichococcus-like strains of this study (NIBRCL0000114567, NIBRCL0000114571) belong to Deuterostichococcus epilithicus and Pseudostichococcus monallantoides respectively in phylogenetic analysis using 18S rDNA sequences. These two species are consistent with recent research in the morphology and the genetic analyses using 18S and ITS rDNA sequences. We reported M. subclavatum, D. epilithicus, and P. monallantoides as newly recorded species in Korea.

• Korean Journal of Pharmacognosy
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• v.13 no.1
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• pp.14-19
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• 1982

Potential toxicity of 15 medicinal plants used for herbal drugs, which were also described as being tonic for hematopoietic system or being toxic for the system in a oriental book 'Dong Ee Bo Gam', were evaluated in mice. Six plants among 15 plants tested appeared to exhibit acute toxicity along with bone marrow depression or with abnormally enhancing the $^3H-thymidine$ incorporation into DNA biosynthesis in bone marrow cells. Six plants were Paeonia albiflora, Pharbitis nil, Cemphalia lapidescens, Scutellaria baicalensis, Akebia quinata and Glycyrriza uralensis.

• Korean Journal of Environmental Biology
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• v.29 no.3
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• pp.138-143
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• 2011

The efficiency of mtCOI amplication after DNA extraction of benthic harpacticoid Tigriopus japonicus s.l. was tested under different conditions depending on fixative (99% Ethanol, or 4% Formalin) and additional chemicals (Ludox or Rose Bengal). Each experimental group by the fixative was subdivided into four groups, respectively: 1) Control (fixative only), 2) processed with Ludox HS40, 3) processed with Rose Bengal, and 4) processed with both Ludox HS40 and Rose Bengal. For the 99% ethanol-fixed sample, overall success rate of amplification by PCR was 96% or above, while for the 4% formalin-fixed one, success rate was much lower than those of ethanol-fixed: 1) Control: 27%, 2) Ludox HS40: 3%, 3) Rose Bengal: 7%, and 4) Ludox HS40 and Rose Bengal: 3%. As a result present study verify that 99% ethanol is a proper fixative for DNA extraction in meiofauna organisms.

• Korean Journal of Fisheries and Aquatic Sciences
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• v.25 no.6
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• pp.474-484
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• 1992

The stock identification of small yellow croaker. Pseudosciaena Polyactis from Mokpo area was carried out using molecular biological methods such as mt-DNA restriction fragment length polymorphism(RFLP) and the N-terminal fragment polymorphism of muscle actin obtained after protease digestion. The entire mt-DNA genomic size from the small yellow croaker at Mokpo area was estimated to be about $16\pm0.2$ Kb. Furthermore, fourteen restriction endonucleases revealed a total of 37 restriction sites to the mt-DNA molecule, however, eight of the fourteen enzymes showed a significant restriction site variation. Six of the enzymes examined produced a single restriction profile for all individuals surveyed, indicating that they don't react on the same mt-DNA obtained from small yellow croaker. The Staphylococcus aureus $V_8$ protease is able to cleave the muscle actin of small yellow croaker and to yield a N-terminal peptide of 26 and 16 KDa, respectively.

• Journal of Microbiology and Biotechnology
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• v.6 no.5
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• pp.331-335
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• 1996

The second $\beta$-Xylosidase gene (xylB) from Bacillus stearothermophilus was isolated from the genomic library, cloned into pBR322, and subsequently transferred into Escherichia coli HB101. Six out of 10, 000 transformants were selected from the selective LB medium supplemented with p-nitrophenyl-$\alpha$-L-arabinofuranoside (pNPAf) and ampicillin ($50\mu g$/ml) based on their ability to form a yellow ring around the colony. One of the clones was found to harbor the recombinant plasmid with 5.0 kb foreign DNA, which was identical to the $\alpha$-L-arabinofuranosidase gene (arfI) previously cloned in this lab, while the other five had 3.5 kb of the foreign DNA. Southern blotting experiments confirmed that the 3.5 kb insert DNA was from B. stearothermophilus chromosomal DNA. A zymogram with 4-methylumbelliferyl-$\alpha$-L-arabinofuranoside as the enzyme substrate revealed that the cloned gene product was one of the mutiple $\alpha$-L-arabinofuranosidases produced by B. stearothermophilus. Unlike the arfI gene product, the product of the gene on the insert DNA (xylB) showed an activity not only on pNPAf but also on oNPX suggesting that the cloned gene product could be a bifunctional enzyme having both $\alpha$-L-arabinofuranosidase and $\beta$-xylosidase activities.

• Animal cells and systems
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• v.11 no.2
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• pp.147-153
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• 2007

DNA extracted from ancient bones of Cervidae animals was examined to identify the species and to determine the phylogenetic relationships to those from extant cervids. Abundant ancient bones were excavated from Kumsung archaeological site in Jeju Island, Korea, and were identified as Cervidae animals based on morphological features of their antlers and lower mandibles. Their mitochondrial DNA (mtDNA) control region (CR) was partially sequenced and subsequently compared with those previously reported in database. The results confirmed that the ancient sequences are lineage of Cervidae. On the phylogenetic trees constructed using the sequence diversity of the CR sequences of family Cervidae, the ancient DNA sequences were found on distinct clusters. The ancient sequences were located in the subfamily Capreolinae cluster, and six ancient sequences were closely related to those of extant Korean roe deer in Jeju Island and Korean Peninsula. Consequently, the results of this study suggest that the roe deer inhabited Jeju Island in ancient times. However, there is no evidence for the existence of subfamily Cervinae, including Sika deer, while it has been described in several historical records. The results suggest that this finding could contribute to understanding of the origin and phylogenetic relationships of extant and ancient roe deer on Jeju Island.

• BMB Reports
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• v.37 no.6
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• pp.657-662
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• 2004

Oligoribonucleotides containing 8-oxo-7,8-dihydroguanosine (8-oxoG) and 8-oxo-7,8-dihydro-2'-O-methylguanosine (8-oxoG-Me) were synthesized. The base pairing properties of 8-oxoG and 8-oxoG-Me in oligoribonucleotide in cDNA synthesis by reverse transcriptases were studied. dCMP was preferentially incorporated into the site opposite 8-oxoG or 8-oxoG-Me than into other dNMPs. TMP and dCMP were inserted preferentially into sites opposite 8-oxoG or 8-oxoG by reverse transcriptases. HIV-RT did not incorporate TMP, but RAV2-RT incorporated 50% more TMP than dCMP into the site opposite 8-oxoG. In the site opposite 8-oxoG-Me TMP was substantially incorporated by HIV-RT or RAV2-RT. Thermodynamic analysis of the DNA. RNA heteroduplex containing 8-oxoG revealed that 8-oxoG and 8-oxoG-Me formed base pairs with cytidine and thymidine with similar stability. The thermodynamic parameter (${\Delta}G^{\circ}$) demonstrated that the formation of duplexes between 8-oxoG or 8-oxoG-Me and cytidine or thymidine is more thermodynamically favorable than with adenosine and guanosine. However, differences in the melting temperature and ${\Delta}G^{\circ}$'s of 8-oxoG/dC and 8-oxoG/T were much smaller than between G/dC and G/T. CD spectra showed that DNA . RNA containing 8-oxoG or 8-oxoG-Me duplexes showed similarities between the A-type RNA and B-type DNA conformations.