• Bulletin of the Korean Chemical Society
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• v.35 no.9
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• pp.2809-2812
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• 2014

The 43-residue defensin-like peptide coprisin, which is isolated from dung bettle, Copris tripartitus, is a potent antimicrobial peptide. In our previous work, we determined the tertiary structure of coprisin and found that alpha helical region of coprisin from residue 19 to residue 30 is important for its antimicrobial activities. Here, we designed cop12mer and cop9mer analogs of coprisin based on the tertiary structure of coprisin. To investigate the relationship between hydrophobicity and antimicrobial activities and develop the potent peptide antibiotics, we designed cop9mer-1 with substitution of $His^2$ with Trp in cop9mer. The results showed that cop9mer-1 has higher toxicities as well as improved antimicrobial activities compared to cop9mer. In order to reduce the toxicity of cop9mer-1, we designed cop9mer-2 and cop9mer-3 with substitution of $Cys^3$ with Lys or Ser. Substitution of $Cys^3$ with these hydrophilic amino acids results in lower cytotoxicities compared to cop9mer-1. Cop9mer-2 with substitution of $Cys^3$ with Lys in Cop9mer-1 showed high antibacterial activities against drug resistant bacteria without cytotoxicity. Antibiotic action of cop9mer-1 analog appears to involve permeabilization of the bacterial cell membrane while cop9mer-2 and cop9mer-3 may have different mechanism of action. These results imply that that optimum balance in hydrophobicity and hydrophilicity in these 9-meric peptides plays key roles in their antimicrobial activities as well as cytotoxicities.

• Proceedings of the Korean Information Science Society Conference
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• 2001.04a
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• pp.748-750
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• 2001

최근 Human Genome Project(HGP)에서 사람의 염기 서열의 초안이 발표되었다. 생물체의 염기 서열을 분석하는 방법은 매우 많은데, 그 중 하나가 k-mer 분석이다. k-mer는 유전자의 염기 서열내의 길이가 k인 연속된 염기 서열이다. k-mer 분석은 염기서열이 가진 k-mer들의 빈도의 분포나 대칭성 등을 탐색하는 것이다. 그런데 유전자의 염기 서열은 대용량 텍스트이고 k가 줄 때 기존의 온메모리 알고리즘으로는 처리가 불가능하므로 효율적인 자료구조와 알고리즘이 필요하다. 본 논문에서는 패턴 일치(pattern matching)에 적합하고 외부 메모리를 지원하는 스트링 B-트리(string B-tree)를 이용한 k-mer 분석 방법을 제시하고, 그것을 구현하였으며 몇 가지 실험 결과에 대하여 기술한다.

• Korean Journal of Microbiology
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• v.44 no.2
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• pp.164-167
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• 2008

Recently, rolling circle amplification (RCA) technique has been widely focused in the field of gene amplification just like PCR method. We have developed RCA-mer, which is a web-based program searching for primer candidates from a given sequence. It can be applied to find primer lists in DNA amplification experiment based on RCA method. The RCA-mer compares 8-mer primer lists with user's input sequence such as vector, mitochondria, and microbial genome sequence. After calculating 8-mers existences in a given sequence, it displays matched and no-matched primer lists with their GC-contents. In addition to it, RCA-mer can search the existence of 8-mer primer lists in two sequences whether they are co-existed or not. Users can apply candidate primer lists to their researches which use RCA techniques.

• Molecules and Cells
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• v.40 no.4
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• pp.262-270
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• 2017

MicroRNAs (miRNAs) are single-stranded, small RNAs (21-23 nucleotides) that function in gene silencing and translational inhibition via the RNA interference mechanism. Most miRNAs originate from host genomic regions, such as intergenic regions, introns, exons, and transposable elements (TEs). Here, we focused on the palindromic structure of medium reiteration frequencies (MERs), which are similar to precursor miRNAs. Five MER consensus sequences (MER5A1, MER53, MER81, MER91C, and MER117) were matched with paralogous transcripts predicted to be precursor miRNAs in the horse genome (equCab2) and located in either intergenic regions or introns. The MER5A1, MER53, and MER91C sequences obtained from RepeatMasker were matched with the eca-miR-544b, eca-miR-1302, and eca-miR-652 precursor sequences derived from Ensembl transcript database, respectively. Each precursor form was anticipated to yield two mature forms, and we confirmed miRNA expression in six different tissues (cerebrum, cerebellum, lung, spleen, adrenal gland, and duodenum) of one thoroughbred horse. MER5A1-derived miRNAs generally showed significantly higher expression in the lung than in other tissues. MER91C-derived miRNA-5p also showed significantly higher expression in the duodenum than in other tissues (cerebellum, lung, spleen, and adrenal gland). The MER117-overlapped expressed sequence tag generated polycistronic miRNAs, which showed higher expression in the duodenum than other tissues. These data indicate that horse MER transposons encode miRNAs that are expressed in several tissues and are thought to have biological functions.

• The KIPS Transactions:PartA
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• v.8A no.4
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• pp.509-516
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• 2001

As results of many genome projects, genomic sequences of many organisms are revealed. Various methods such as global alignment, local alignment are used to analyze the sequences of the organisms, and k -mer analysis is one of the methods for analyzing the genomic sequences. The k -mer analysis explores the frequencies of all k-mers or the symmetry of them where the k -mer is the sequenced base with the length of k. However, existing on-memory algorithms are not applicable to the k -mer analysis because a whole genomic sequence is usually a large text. Therefore, efficient data structures and algorithms are needed. String B-tree is a good data structure that supports external memory and fits into pattern matching. In this paper, we improve the string B-tree in order to efficiently apply the data structure to k -mer analysis, and the results of k -mer analysis for C. elegans and other 30 genomic sequences are shown. We present a visualization system which enables users to investigate the distribution and symmetry of the frequencies of all k -mers using CGR (Chaotic Game Representation). We also describe the method to find the signature which is the part of the sequence that is similar to the whole genomic sequence.

• Journal of Microbiology and Biotechnology
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• v.20 no.5
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• pp.917-924
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• 2010

The practicability of transgenic tobacco engineered to express bacterial native mercuric reductase (MerA), responsible for the transport of $Hg^{2+}$ ions into the cell and their reduction to elemental mercury ($Hg^0$), without any codon modification, for phytoremediation of mercury pollution was evaluated. Transgenic tobacco plants reduce mercury ions to the metallic form; take up metallic mercury through their roots; and evolve the less toxic elemental mercury. Transformed tobacco produced a large amount of merA protein in leaves and showed a relatively higher resistance phenotype to $HgCl_2$ than wild type. Results suggest that the integrated merA gene, encoding mercuric reductase, a key enzyme of the bacterial mer operon, was stably integrated into the tobacco genome and translated to active MerA, which catalyzes the bioconversion of toxic $Hg^{2+}$ to the least toxic elemental $Hg^0$, and suggest that MerA is capable of reducing the $Hg^{2+}$, probably via NADPH as an electron donor. The transgenic tobacco expressing merA volatilized significantly more mercury than wild-type plants. This is first time we are reporting the expression of a bacterial native merA gene via the nuclear genome of Nicotiana tabacum, and enhanced mercury volatilization from tobacco transgenics. The study clearly indicates that transgenic tobacco plants are reasonable candidates for the remediation of mercurycontaminated areas.

• Korean Journal of Microbiology
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• v.52 no.4
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• pp.428-436
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• 2016

The emergence of antibiotic-resistant bacteria has been increased and become a public health concern worldwide. Many bacterial infections can be sequentially treated with different types of antibiotics. Thus, this study was designed to evaluate the changes in survival, antibiotic susceptibility, mutant frequency, ${\beta}$-lactamase activity, biofilm formation, and gene expression in Klebsiella pneumoniae after exposure to sequential antibiotic treatments of ciprofloxacin and meropenem. Treatments include control (CON; no addition), 1/2 MIC ciprofloxacin addition (1/2CIP), 2 MIC ciprofloxacin addition (2CIP), initial 1/2 MIC ciprofloxacin addition followed by 1/2 MIC meropenem (8 h-incubation) and 2 MIC ciprofloxacin (16 h-incubation) (1/2CIP-1/2MER-2CIP), initial 1/2 MIC ciprofloxacin addition followed by 1/2 MIC meropenem (8 h-incubation) and 2 MIC meropenem (16 h-incubation) (1/2CIP-1/2MER-2MER), and initial 1/2 MIC ciprofloxacin addition followed by 2 MIC ciprofloxacin(8 h-incubation) and 2 MIC meropenem(16 h-incubation) (1/2CIP-2CIP-2MER). No growth of K. pneumoniae was observed for the 2CIP throughout the incubation period. The numbers of planktonic cells varied with the treatments (7~10 log CFU/ml), while those of biofilm cells were not significantly different among treatments after 24-h incubation, showing approximately 7 log CFU/ml. Among the sequential treatments, the least mutant frequency was observed at the 1/2CIP-1/2MER-2CIP (14%). Compared to the CON, 1/2CIP-2CIP-2MER decreased the sensitivity of K. pneumoniae to piperacillin, cefotaxime, and nalidixic acid. The highest ${\beta}$-lactamase activity was 22 nmol/min/ml for 1/2CIP-1/2MER-2CIP, while the least ${\beta}$-lactamase activity was 6 nmol/min/ml for 1/2CIP-2CIP-2MER. The relative expression levels of multidrug efflux pump-related genes (acrA, acrB, and ramA) were increased more than 2-fold in K. pneumoniae exposed to 1/2CIP-1/2MER-2MER and 1/2CIP-2CIP-2MER. The results suggest that the sequential antibiotic treatments could change the antibiotic resistance profiles in K. pneumoniae.

• Journal of Plant Biotechnology
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• v.35 no.4
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• pp.291-298
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• 2008

Methylmercury, an organic derivative, is the principal form of mercury that biomagnifies and causes neurodegenerative symptoms in animals. In recent years, living modified organism (LMO) resulting from biotechnology has played a highly visible and controversial role. Despite the potential benefits of this technology, public concerns have been raised about the environmental risk of LMO. The concern on the risk from LMO release has urged efforts to evaluate and manage the risks of the LMO. To build up the capacity building of risk assessment method for LMO used environmental remediation, we engineered Solanum nigrum L, expressing the modified bacterial gene, merB, encoding organomercurial lyase. Two independently isolated transgenic lines produced merB RNA. Transgenic Solanum nigrum leaf discs expressing merB gene showed organic mercury resistance, forming shoots well on growth medium containing $0.5{\mu}M$ methylmercury (II) chloride and $1{\mu}M$ phenylmercuric acetate while control plants breached. Transgenic merB seeds germinated and grew on growth medium containing $2{\mu}M$ methylmercury (II) chloride and phenylmercuric acetate. The merB transgenic plants will be used for risk assessment of natural environment.

• Journal of the Korean Chemical Society
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• v.45 no.5
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• pp.436-441
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• 2001

The emission and excitation spectra of mer-[Cr(dien)(glygly)]ClO$_4$(glygly=glycylglycinate;dien=N-(2-aminoethyl)-1,2-ethanediamine) taken at 77 K are reported. The infrared and visible spectra at 298 K are also measured. The twelve electronic bands due to spin-allowed and spin-forbidden transitions are assigned. Using the observed transitions, a ligand field analysis has been performed to determine the bonding property of coordinated atoms in the chromium(III) complex. It is confirmed that the amine nitrogen atoms of the dien and glygly have strong $\sigma$-donor characters, but the peptide nitrogen of glygly has weak $\pi$-donor property toward chromium(III) ion.

• Bulletin of the Korean Chemical Society
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• v.33 no.1
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• pp.183-188
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• 2012

A blue phosphorescent $Ir(dfpypy)_3$ (dfpypy:fluorinated pyridine-pyridine ligand) complex with meridional configuration has been synthesized by newly developed effective method and its solid state structure and photoluminescence are characterized. For this complex, mer-$Ir(dfpypy)_3$, the glass-transition and decomposition temperatures appear at $160^{\circ}C$ and $384^{\circ}C$ respectively in TGA and DSC experiments, which indicates that this complex has high thermal stability. In a crystalline structure, an average Ir-C bond length of mer-$Ir(dfpypy)_3$ is slightly longer than that of fac-$Ir(dfpypy)_3$, which assumed to be due to the weak trans-influence. The absorption and emission spectra are observed more red-shifted in mer-$Ir(dfpypy)_3$ than fac-$Ir(dfpypy)_3$. In addition, the former is readily oxidized than the latter in electrochemical behavior.