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

• Journal of the Institute of Electronics and Information Engineers
• /
• v.52 no.7
• /
• pp.51-62
• /
• 2015

Of recent interests on high capacity DNA storage, DNA watermarking for DNA copyright protection, and DNA steganography for DNA secret communication are augmented, the reversible DNA watermarking is much needed both to embed the watermark without changing the functionality of organism and to perfectly recover the host DNA sequence. In this paper, we address two ways of DE based reversible DNA watermarking using noncoding DNA sequence. The reversible DNA watermarking should consider the string structure of a DNA sequence, the organism functionality, the perfect recovery, and the high embedding capacity. We convert the string sequence of four characters in noncoding region to the decimal coded values and embed the watermark bit into coded values by two ways; DE based multiple bits embedding (DE-MBE) using pairs of neighbor coded values and consecutive DE-MBE (C-DE-MBE). Two ways process the comparison searching to prevent the false start codon that produces false coding region. Experimental results verified that our ways have more high embedding capacity than conventional methods and produce no false start codon and recover perfectly the host sequence without the reference sequence. Especially C-DE-MBE can embed more high two times than DE-MBE.

• Applied Biological Chemistry
• /
• v.45 no.3
• /
• pp.129-133
• /
• 2002

Suppression of nitrate accumulation in spinach and lettuce through foliar application of chitosan formula containing micronutrients is related with the increase of the nitrate reductase (NR) activity. If NR in spinach were highly expressed to increase the assimilatory activity, nitrate content could be reduced. For this, NR cDNA was cloned from the isolated mRNAs of spinach using reverse transcriptase-PCR. Nucleotide sequence of cloned spinach NR cDNA showed highly deduced amino acid sequence identity ($71{\sim}82%$) with other known plant NR genes. Only two nucleotide-base differences were observed in the cloned NR cDNA compared with that of the published spinach NR cDNA.

• Korean Journal of Microbiology
• /
• v.40 no.2
• /
• pp.65-72
• /
• 2004

Instability of some eukaryotic sequence propagated in prokaryotic hosts is a frequently observed phenomenon. It is well documented that long inverted repeats, AT-rich sequences with structures like Z-DNA are extremely unstable in E. coli. These sequences may either be under-represented or even lost when cloned in E. coli. When we analyzed the polymorphic pattern for several tandom repeat (TR) in human SCKI gene, we found some TR regions were frequently deleted from plasmids and had difficult problem for their sequencing. These regions may result in non-clonability of the DNA sequence. Here we have cloned two difficult TR regions under low temperature and made two library for DNA sequencing using a nebulizer or sonicator. This study will help to determine the unstable genomic elements in complex mammalian genome.

• Korean Journal of Microbiology
• /
• v.55 no.3
• /
• pp.220-225
• /
• 2019

Studies based on microbial community analyses have increased in the recent decade since the development of next generation sequencing technology. Associations of gut microbiota with host's health are one of the major outcomes of microbial ecology filed. The major approach for microbial community analysis includes the sequencing of variable regions of 16S rRNA genes, which does not provide the information of bacterial activities. Here, we conducted RNA-based microbial community analysis and compared results obtained from DNA- and its cDNA-based microbial community analyses. Our results indicated that these two approaches differed in the ratio of Firmicutes and Bacteroidetes, known as an obesity indicator, as well as abundance of some key bacteria in gut metabolisms such as butyrate producers and probiotics strains. Therefore, cDNA-based microbial community may provide different insights regarding roles of gut microbiota compared to the previous studies where DNA-based microbial community analyses were performed.

• Journal of Life Science
• /
• v.22 no.8
• /
• pp.1120-1125
• /
• 2012

Cirsium pendulum plants were collected from Hongcheon, Pyeongchang, Wonju, Yangyang in Kangwondo, Gapyeong in Gyeongkido, and Choongju in Choongcheongbukdo. Cirsium setidens plants were collected from Taebaek in Kangwondo and Bonghwa in Kyeongsangbukdo. Genomic DNA was prepared from those plants and used for the amplification of 18S rDNA, ITS1, 5.8S rDNA, ITS2, and part of 28S rDNA. The PCR products were sequenced, and the sequence was deposited in the GenBank. The comparison of those sequences has revealed that the rDNA sequences are identical for all six C. pendulum plants, but that the ITS1 and ITS2 sequences contain variable nucleotides. The two C. setidens plants had different nucleotides in 18S rDNA, ITS1, and ITS2. The comparison of the DNA sequences of C. pendulum and C. setidens collected in this study with C. pendulum of Hokkaido in Japan and C. japonicum of Anhui in China indicated that the plants of those three species are clearly divided into three distinct groups. The silymarin content of the collected plants was analyzed and turned out to be quite high. Therefore, it has been found that both C. pendulum and C. setidens plants are producing large amounts of silymarin, which has been reported to have various medicinal effects.

• Proceedings of the Korean Information Science Society Conference
• /
• 2004.10b
• /
• pp.298-300
• /
• 2004

기존의 생물정보학 연구는 전체 서열들의 매칭을 통한 상동성 연구에 중점을 두고 진행되어 왔다 최근에 서열 데이터베이스의 급격한 증가와 게놈 정보가 축적됨에 따라 서열로부터 다양한 정보를 얻기 위해 서열 데이터 분석에 마이닝 기법을 접목시키고자 하는 다양한 기술들이 제안되고 있다. 단백질과 DNA의 서열 비교는 생물정보학의 기본 작업 기운데 하나이다. 신속하고 자동화 된 서열 비교 능력은 새로운 서열에 대한 기능 판별 및 분석 등 모든 작업을 용이하게 한다 본 논문에서는 동종의 단백질 서열들을 다중 정렬하여 일치하는 구간을 찾아내고, 그 구간에서 아미노산 코드와 위치정보를 이용해 동종 서열들 간의 특정한 패턴 규칙을 찾아내고, 새로운 서열에서 어떤 서열 필턴 특징이 발생하는지를 찾아냄으로써 서얼을 분류하는 방법을 제안한다.

• Journal of the Institute of Electronics and Information Engineers
• /
• v.51 no.10
• /
• pp.118-127
• /
• 2014

DNA data storage refers to any technique for storing massive digital data in base sequence of DNA and has been recognized as the future storage medium recently. This paper presents an information hiding method for DNA data storage that the massive data is hidden in non-coding strand based on DNA steganography. Our method maps the encrypted data to the data base sequence using the numerical mapping table and then hides it in the non-coding strand using the key that consists of the seed and sector length. Therefore, our method can preserve the protein, extract the hidden data without the knowledge of host DNA sequence, and detect the position of mutation error. Experimental results verify that our method has more high data capacity than conventional methods and also detects the positions of mutation errors by the parity bases.

• Korean Journal of Plant Resources
• /
• v.24 no.5
• /
• pp.584-590
• /
• 2011

Wound inducible P450-Esg cDNA, one of cytochrome P450 gene family, was isolated from shoot of Euiseong garlic cultivar. P450-Esg cDNA possesses highly conserved heme-binding domain in the nucleotide sequence, and 1,419 bp of open reading frame (ORF) coding of 473 amino acids. Based on the nucleotide sequence analysis of P450-Esg homologous from twelve garlic cultivars, two domains, one domain between 472 to 510 bp, and the other between 1,210 to 1,249 bp from start codon (ATG), showed various nucleotide polymorphism among cultivars. Sequence of heme-binding domain in P450-Esg homologous, which is located at the domain between 1,210 to 1,240 bp from start codon, showed various nucleotide polymorphism as well as amino acid sequence polymorphism among twelve garlic cultivars. Anther domain, between 472 to 510 bp from start codon, showed exactly same amino acid sequence in the twelve garlic cultivars, but there were various single nucleotide polymorphism to the cultivars.

• Clinical and Experimental Pediatrics
• /
• v.53 no.3
• /
• pp.397-407
• /
• 2010

Purpose : The F9 gene is known to be the causative gene for hemophilia B, but unfortunately the detection rate for restriction fragment length polymorphism-based linkage analysis is only 55.6%. Direct DNA sequencing can detect 98% of mutations, but this alternative procedure is very costly. Here, we conducted multiplex polymerase chain reactions (PCRs) and conformation sensitive gel electrophoresis (CSGE) to perform a screened DNA sequencing for the F9 gene, and we compared the results with direct sequencing in terms of accuracy, cost, simplicity, and time consumption. Methods : A total of 27 unrelated hemophilia B patients were enrolled. Direct DNA sequencing was performed for 27 patients by a separate institute, and multiplex PCR-CSGE screened sequencing was done in our laboratory. Results of the direct DNA sequencing were used as a reference, to which the results of the multiplex PCR-CSGE screened sequencing were compared. For the patients whose mutation was not detected by the 2 methods, multiplex ligation-dependent probe amplification (MLPA) was conducted. Results : With direct sequencing, the mutations could be identified from 26 patients (96.3%), whereas for multiplex PCRCSGE screened sequencing, the mutations could be detected in 23 (85.2%). One patient's mutation was identified by MLPA. A total of 21 different mutations were found among the 27 patients. Conclusion : Multiplex PCR-CSGE screened DNA sequencing detected 88.9% of mutations and reduced costs by 55.7% compared with direct DNA sequencing. However, it was more labor-intensive and time-consuming.