• 한국생물공학회:학술대회논문집
• /
• 2000.04a
• /
• pp.153-156
• /
• 2000

Xylan, the major hemicellulose component of many plants, occurs naturally in a partially acetylated form and lignin, the most resistant component in plant cell wall degradation, is also attached to ${\beta}-1,4-linked-D-xylose$ backbone through the ester linkage. Esterases are required to release the esterified substituent and acetyl esterases are important in the complete degradation of acetylated polysaccharides, like pectins and xylans. The gene(Axe) encoding acetyl xylan estarase(AXE) was isolated from genomic ${\lambda}$ library from Aspergillus ficuum. Nucleotide sequencing of the Axe gene indicated that the gene was separated with two intervening sequences and the amino acid sequence comparison revealed that it was closely related to that from A. awamori with the 92 % indentity. Heterologous expression of AXE was conducted by using YEp352 and Saccharomyces cerevisae 2805 as a vector and host expression system, respectively. The Axe gene was placed between GAL1 promoter and GAL7 terminator and then this recombinant vector was used to transform S. cerevisiae 2805 strain. Culture filtrate of the transformed yeast was assayed for the presence of AXE activity by spectrophotometry and, comparing with the host strain, four to five times of enzyme activity was detected in culture filtrate of transformed yeast.

• Parasites, Hosts and Diseases
• /
• v.53 no.4
• /
• pp.455-463
• /
• 2015

The present study was performed to compare the mitochondrial genomes between 2 Spirometra tapeworms, Spirometra erinaceieuropaei and Spirometra decipiens (Cestoidea: Diphyllobothriidae), which larval stages are important etiological agents of sparganosis in humans. For each species, the full mitochondrial genome was amplified in 8 overlapping fragments using total genomic DNA purified from a single worm as the template. The mitochondrial genomes were 13,643 bp (S. erinaceieuropaei) and 13,641 bp (S. decipiens) in length and contained 36 genes; 12 protein-coding genes, 2 ribosomal RNA (rRNA, small and large subunits), and 22 transfer RNAs (tRNAs). The 12 protein-coding genes constituted 10,083 bp (S. erinaceieuropaei) and 10,086 bp (S. decipiens) of their respective mitochondrial genomes. The tRNA genes, ranging in length from 56 to 70 bp, were identified based on putative secondary structures such as the typical cloverleaf shape. A total of 23 intergenic sequences, varying from 1 to 204 bp in size, were interspersed in S. erinaceieuropaei (total, 504 bp) and S. decipiens (total, 496 bp) mtDNA. The 12 protein-coding genes of S. erinaceieuropaei and S. decipiens differed by 12.4%, whereas the overall difference in mtDNA sequence between S. erinaceieuropaei and S. decipiens was 12.9%. Thus, from the standpoint of the mitochondrial genome, S. decipiens represents a valid species that can be distinguished from S. erinaceieuropaei.

• Journal of Microbiology
• /
• v.38 no.2
• /
• pp.80-87
• /
• 2000

The nucleotide sequence of the luxC gene coding for lux-specific fatty acyl-CoA reductase and the upstream DNA (325bp)of the structural gene from bioluminescent bacterium, Photobacterium phosphoreum, has been deternubed. An open reading frame extending for more than 20 codons in 325 bp DNA upstream of luxC was not present in both directions. The lux gene can be translated into a polypeptide of 54 kDa and the amino acid sequences of lux specific reductases of P. phosphoreum shares 80, 65, 58, and 62% identity with those of the Photobacterium leiognathi, Vibrio fischeri, Vibrio harveyi, and Xehnorhabdus luminescenens reductases, respectively. Analyses of codon usage, showing that a high frequency (2.3%) of the isoleucine codon, AUA, in the luxC gene compared to that found in Escherichia coli genes (0.2%) and its absence in the luxA and B genes, suggested that the AUA codon may play a modulator role in the expression of lux gene in E. coli. The structural genes (luxC, D, A, B, E) of the P. phosphoreum coding for luciferase (${\alpha}$,${\beta}$) and fatty acid reductase (r, s, t) polypeptides can be expressed exclusively in E. coli under the T7 phage RNA polymerase/promoter system and identificationof the [35S]methionine labelled polypeptide products. The degree of expression of lux genes in analyses of codon usage. High expression of the luxC gene could only be accomplished in a mutant E. coli 43R. Even in crude extracts, the acylated acyl-CoA reductase intermediate as well as acyl-CoA reductrase activities could be readily detected.

• Proceedings of the KIEE Conference
• /
• 1999.11c
• /
• pp.576-578
• /
• 1999

본 논문에서는 생물학적인 DNA와 유전자 알고리즘의 진화 메커니즘에 근거를 둔 DNA 코딩방법을 변형하여 새로운 DNA 코딩 방법을 제안한다. 이 방법은 기존의 DNA 코딩 방법이 DNA 유전자의 Redundancy와 Over-lapping 성질 때문에 갖고 있는 DNA 자체의 특성인 염색체의 길이를 자유자재로 변화시킬 수 있는 코딩 기술에 진화단계에서 변형을 가할 수 있는 새로운 유전자 알고리즘을 추가하여, 초기에 국소해로 접근하는 일반적인 유전자 알고리즘의 위험 부담률을 줄이고, 전역 해로의 접근 가능성을 높이는 방법을 제시한다. 또한. 이 변형된 DNA 코딩 방법의 가능성을 입증하기 위하여 시스템 제어에 필요한 지식을 표현하는 적당한 퍼지 규칙을 후건부의 매개변수의 동조만을 통하여 획득하고, 이 규칙에 변형된 DNA 코딩 방법을 적용하여 최적화 된 새로운 퍼지규칙 획득 알고리즘을 개발한다. 제안된 알고리즘을 이용한 퍼지 제어기를 설계하고. 이 제어기의 유용성을 입증하기 위하여 병렬형 이중 도립진자 시스템에 적용하여 시뮬레이션을 실행한 결과 효과적으로 퍼지규칙을 획득하고 제어함을 알 수 있다.

• Journal of Korea Multimedia Society
• /
• v.20 no.2
• /
• pp.244-253
• /
• 2017

Reversible DNA watermarking is capable of continuous DNA storage and forgery prevention, and has the advantage of being able to analyze biological mutation processes by external watermarking by iterative process of concealment and restoration. In this paper, we propose a reversible DNA watermarking method based on histogram multiple shifting of noncoding DNA sequence that can prevent false start codon, maintain original sequence length, maintain high watermark capacity without biologic mutation. The proposed method transforms the non-coding region DNA sequence to the n-th code coefficients and embeds the multiple bits of the n-th code coefficients by the non-recursive histogram multiple shifting method. The multi-bit embedding process prevents the false start codon generation through comparison search between adjacent concealed nucleotide sequences. From the experimental results, it was confirmed that the proposed method has higher watermark capacity of 0.004-0.382 bpn than the conventional method and has higher watermark capacity than the additional data. Also, it was confirmed that false start codon was not generated unlike the conventional method.

• Korean Journal of Plant Taxonomy
• /
• v.41 no.3
• /
• pp.194-201
• /
• 2011

In order to acquire information on chloroplast DNA markers to evaluate the genetic diversity of evergreen broad leaved plants, we investigated the intraspecific variation of cpDNA in eight non-coding regions of nine species commonly distributed in East Asia. Although no variations were detected in psbA-trnH, rpoB-trnC, rpl16 and atpB-rbcL regions, a relatively large amount of intraspecific variations was detected in the psbC-trnS, rps16 and trnL-F regions. These results suggested that these three cpDNA markers are suitable to assess genetic diversity of the species investigated in this study. In contrast, intraspecific variations were detected in seven taxa except Hedera rhombea and Neolitsea aciculata. Neolitsea sericea and the taxa of Quercus had many polymorphic sites.

• Journal of Applied Biological Chemistry
• /
• v.56 no.1
• /
• pp.37-42
• /
• 2013

In eukaryotes, most of the genome are transcribed, however only a small proportion of total transcripts encodes for protein, thus resulting in many of noncoding RNAs. In order to recover DNA damage including DNA double-strand breaks (DSBs) eukaryotes have evolved complex mechanisms and these are processed through coordinated mechanisms of protein sensors, transducers, and effectors including RNAs. During recent years, small RNAs have been increasingly studied and gradually considered as key regulators in various aspects of biology. Upon DNA damage, small RNAs including diRNAs (DSB induced RNA) are generated in both plant and human cell lines. Inhibition of their biogenesis has severe influence on DSB repair system.

• Genomics & Informatics
• /
• v.16 no.4
• /
• pp.27.1-27.6
• /
• 2018

The non-coding DNA in eukaryotic genomes encodes a language that programs chromatin accessibility, transcription factor binding, and various other activities. The objective of this study was to determine the effect of the primary DNA sequence on the epigenomic landscape across a 200-base pair of genomic units by integrating 127 publicly available ChromHMM BED files from the Roadmap Genomics project. Nucleotide frequency profiles of 127 chromatin annotations stratified by chromatin variability were analyzed and integrative hidden Markov models were built to detect Markov properties of chromatin regions. Our aim was to identify the relationship between DNA sequence units and their chromatin variability based on integrated ChromHMM datasets of different cell and tissue types.

• Journal of Applied Biological Chemistry
• /
• v.43 no.1
• /
• pp.5-11
• /
• 2000

Three cDNA clones encoding rice calmodulin (CaM) isoforms (OsCaM-1, OsCaM-2, and OsCaM-3) were isolated from a rice cDNA library constructed from suspension-cultured rice cells treated with fungal elicitor. The coding regions of OsCaM-1 and O.sCaM-2 were 89% homologous at DNA Ievel, whereas the 5' and 3' untranslated regions were highly divergent. The polypeptides encoded by OsCaM-1 and OsCaM-2 was identical except two conservative substitution at position 8 and 75. The coding region of OsCaM-3 was consist of a typical conserved CaM domain and an additional C-terminal extension. The amino acid sequence of conserved CaM domain of OsCaM-3 shared only 86% identity with that OsCaM-1. The OsCaM-3 cDNA is belongs to a novel group of calmodulin gene due to its C-terminal extension of 38 amino acids, a large number of which are positively charged. The extension also contains a C-terminal CaaX-box prenylation site (CVlL). Genomic Southern analysis revealed at least six copies of CaM or CaM-related genes, suggesting that calmodulin may be represented by a small multigene family in the rice geneme. Expression of OsCaM gene was examined through Northern blot analysis. Transcript level of OsCaM-3 was increased by treatment with a fungal elicitor, whereas the OsCaM-1 and OsCaM-2 genes did not respond to the fungal elicitor. The expression of OsCaM-3 gene was remarkable inhibited in the rice cells treated with cyclosporine A, calcinurin inhibitor.

• Journal of Life Science
• /
• v.12 no.2
• /
• pp.188-199
• /
• 2002

A gene coding for xylanase from thermo-tolerant Bacillus pumilus TX703 was cloned into Escherichia coli DH5 $\alpha$ using pUC19. Among 7,400 transformants, four transformants showed clear zones on the detection agar plates containing oat-spells xylan. One of them which showed highest xylanase activity was selected and its recombinant plasmid, named pXES106, was found to carry 2.24 kb insert DNA fragment. When the nucleotide sequence of the cloned xylanase gene (xynK) was determined, xynK gene was found to consist of 1,227 base-pair open reading frame coding for a polypeptide of 409 amino acids with a deduced molecular weight of 48 kDa. The coding sequence was preceded by a putative ribosome binding site, the transcription initiation signals, and cia-acting catabolite responsive element. The deduced amino acids sequence of xylanase is similar to those of the xylanases from Hordeum vulgare (barley) and Clostridium thermocellum, with 39 and 31% identical residues, respectively. The amino acids sequence of this xylanase was quite different from those of the xylanases from other Bacillus species.