• Journal of Microbiology
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• v.45 no.5
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• pp.466-472
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• 2007

A total of 98 vancomycin-resistant Enterococcus faecium (VREF) isolates (58 isolates from patients and 40 isolates from poultry) were compared based on their antimicrobial susceptibility, Tn1546 element organization, and pulsed-field gel electrophoresis (PFGE) patterns. This comparison aided in determining the relationships between the groups of isolates. All the VREF isolates harbored the vanA gene; however, 29 (29.6%) of the isolates exhibited the VanB phenotype-vanA genotype. Furthermore, the VREF isolates from humans and poultry exhibited distinct antimicrobial resistance patterns. The PCR mapping of the Tn1546 elements exhibited 12 different transposon types (A to L). The VREF isolates of poultry were classified into types A to D, whereas the human isolates were classified into types E to L. A PFGE analysis demonstrated a high degree of clonal heterogeneity in both groups of isolates; however, the distinct VREF clones appeared in each group of isolates. The deletion of the vanX-vanY genes or insertion of IS1216V in the intergenic region from the vanX-vanY genes is directly associated with the incongruence of the VanB phenotype-vanA genotype in human VREF isolates. These data suggest that the VREF isolates exhibit distinct phenotypic and genotypic traits according to their origins, which suggests that no evidence exists to substantiate the clonal spread or transfer of vancomycin resistance determinants between humans and poultry.

• Genomics & Informatics
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• v.13 no.3
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• pp.81-85
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• 2015

Molecular characterization technology in genetically modified organisms, in addition to how transgenic biotechnologies are developed now require full transparency to assess the risk to living modified and non-modified organisms. Next generation sequencing (NGS) methodology is suggested as an effective means in genome characterization and detection of transgenic insertion locations. In the present study, we applied NGS to insert transgenic loci, specifically the epidermal growth factor (EGF) in genetically modified rice cells. A total of 29.3 Gb (${\sim}72{\times}coverage$) was sequenced with a $2{\times}150bp$ paired end method by Illumina HiSeq2500, which was consecutively mapped to the rice genome and T-vector sequence. The compatible pairs of reads were successfully mapped to 10 loci on the rice chromosome and vector sequences were validated to the insertion location by polymerase chain reaction (PCR) amplification. The EGF transgenic site was confirmed only on chromosome 4 by PCR. Results of this study demonstrated the success of NGS data to characterize the rice genome. Bioinformatics analyses must be developed in association with NGS data to identify highly accurate transgenic sites.

• Journal of the Korea Institute of Information and Communication Engineering
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• v.19 no.2
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• pp.365-371
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• 2015

CB tree represents the binary trie by a compact binary sequence. However, retrieval time grows fast since the more keys stored in the trie, longer the binary sequences are. In addition it is inefficient for frequent key insertion/deletion. HCB tree is a hierarchical CB tree consisting of small binary tries. However it can not avoid shift operations and have to scan an additional table to refer child or parent trie. In order to improve retrieval performance and avoid shift operations when keys are inserted or deleted, we in this paper represent each separated trie by a full binary trie and then assign the unique identifier to it. Finally the theoretical evaluations show that both the proposed approach and HCB tree provides better than CB tree for key retrieval. The proposed approach shows the highest performance in case of key insertion/deletion and moreover requires only 71%~89% of storage as compared with CB tree.

• Journal of Microbiology and Biotechnology
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• v.16 no.7
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• pp.1097-1103
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• 2006

The divalent antibody-toxins are expected to have increased binding avidities to target cells because of the two cell-binding domains. However, previous studies showed that the refolding yield of divalent antibody-toxin is very low, and it is assumed that homodimer formation of antibody-toxin is strongly interfered by the repulsion between the two large toxin domains that come close to each other during dimer formation. In this study, B3 antibody was used as a model antibody, and its Fab domain was used to construct three different kinds of Fab divalent molecules, $[B3(Fab)-toxin]_{2}$. The monomer Fab-toxin molecules were made by fusing the Fab domain of monoclonal antibody B3 to PE38, a truncated mutant form of Pseudomonas exotoxin (PE), and a connecting sequence that contained spacer amino acid sequence (G4S)n (n=l, 2, 3) was inserted between Fab and PE38. The prepared divalent molecules were $[Fab-S\;1,\;2,\;3-PE38]_{2}\;(=[Fab-SKPCIST-KAS(G_{4}S)nGGPE-PE38]_{2}\;(n=1,\;2,\;3))$, and they are derivatives of previously studied $[Fab-H2cys-PE38]_{2}\;(=[Fab-SKPCIST-KASGGPE-PE38]_{2})$. In $[Fab-Sl,\;2,\;3-PE38]_{2}$, two Fab-S1, 2, 3-PE38 monomers were covalently linked by the disulfide bond bridge made from cysteine in the -SKPCIST- sequence. The insertion of spacer amino acids after the disulfide bridge resulted in a 12-18 fold higher yield of dimer formation than previously constructed $[Fab-Hlcys-PZ38]_{2}[7]$, 3-4-fold higher than $[Fab-ext-PZ38]_{2}[25]$. These two molecules have less amino acid spacer sequence between the disulfide bridge and PE38 domain. The design of $[Fab-PE38]_{2}$ in this study gave molecules with a higher refolding yield. The results of cytotoxicity assay showed a higher cytotoxic effect of these divalent molecules than that of the monovalent scFv-PE38 molecule.

• Journal of Plant Biotechnology
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• v.41 no.3
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• pp.127-133
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• 2014

Four transgenic rice lines harboring insect-resistant gene cry3A showed ideal field performances characterized by high considerable resistance to rice water weevil (Lissorhoptrus oryzophilus Kuschel). In this study, we estimated the insertion number of foreign genes, and analyzed the flanking sequences of T-DNAs in rice genome. As a result, T-DNA of BT12R1 line was inserted in exon region of rice chromosome 10. Two copies of T-DNAs were inserted in line BT12R2. BT12R3 line was analyzed at only left border flanking sequence. BT12R4 line was confirmed one copy of foreign gene insertion at the position 24,516,607 ~ 24,516,636 of rice chromosome 5, accompanied by a deletion of 30 bp known genomic sequences. This intergenic position was confirmed none of expressed gene and any deletion/addition of T-DNA sequence. In conclusion, these molecular data of rice water weevil resistant Bt rice would be used to conduct the biosafety and environment risk assessment for GM crop commercialization.

• Molecules and Cells
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• v.20 no.3
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• pp.385-391
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• 2005

As a first step towards identifying genes involving in the signal transduction pathways mediating rice blast resistance, we isolated 3 mutants lines that showed enhanced susceptibility to rice blast KJ105 (91-033) from a T-DNA insertion library of the japonica rice cultivar, Hwayeong. Since none of the susceptible phenotypes co-segregated with the T-DNA insertion we adapted a map-based cloning strategy to isolate the gene(s) responsible for the enhanced susceptibility of the Hwayeong mutants. A genetic mapping population was produced by crossing the resistant wild type Hwayeong with the susceptible cultivar, Nagdong. Chi-square analysis of the $F_2$ segregating population indicated that resistance in Hwayeong was controlled by a single major gene that we tentatively named Pi-hy. Randomly selected susceptible plants in the $F_2$ population were used to build an initial map of Pi-hy. The SSLP marker RM2265 on chromosome 2 was closely linked to resistance. High resolution mapping using 105 $F_2$ plants revealed that the resistance gene was tightly linked, or identical, to Pib, a resistance gene with a nucleotide binding sequence and leucine-rich repeats (NB-LRR) previously isolated. Sequence analysis of the Pib locus amplified from three susceptible mutants revealed lesions within this gene, demonstrating that the Pi-hy gene is Pib. The Pib mutations in 1D-22-10-13, 1D-54-16-8, and 1C-143-16-1 were, respectively, a missense mutation in the conserved NB domain 3, a nonsense mutation in the 5th LRR, and a nonsense mutation in the C terminus following the LRRs that causes a small deletion of the C terminus. These findings provide evidence that NB domain 3 and the C terminus are required for full activity of the plant R gene. They also suggest that alterations of the resistance gene can cause major differences in pathogen specificity by affecting interactions with an avirulence factor.

• Korean Journal of Plant Resources
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• v.36 no.4
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• pp.290-298
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• 2023

Several members of the genus Broussonetia are woody plants with high-quality cellulose fibers and are used to make a traditional type of Korean paper known as Hanji. Three of these species, Broussonetia kazinoki, Broussonetia monoica, and Broussonetia papyrifera, are found in the Korean Peninsula. Because it is challenging to distinguish different Broussonetia species based on morphology alone, we have developed a set of insertion/deletion (InDel) markers for genetic identification of these species. From twenty-two Broussonetia samples collected throughout Korea, we selected six for next-generation sequencing analysis. InDel marker candidates were identified by comparing this sequence information with the B. kazinoki chloroplast genome sequence. The marker candidates were used to screen the genomes of the twenty-two Broussonetia plants, and five useful chloroplast-based InDel markers were identified. Detailed genotyping using these five markers showed that the twenty-two plants of the genus Broussonetia could be clustered into five groups, verifying that the markers developed here can be used for breeding, identification, and analysis of species in the genus Broussonetia.

• The Journal of Korean Institute of Electromagnetic Engineering and Science
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• v.21 no.1
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• pp.1-7
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• 2010

PAPR of the pilot symbols can be reduced down by the CAZAC sequence in the SC-FDMA communication system. However, it is very complicated and takes quite a long time to compute the interpolation between the OFDM information symbols for the channel estimation because the pilot data are trasmitted in the block type. Furthermore, situation will be much more serious in the severe fading channel. Actually the pilot insertion of the comb type is much efficient and convenient for the channel estimation since the calculation of the interpolation can be made in the frequency domain symbol by symbol. But, the PAPR will be regrown when the pilot data are inserted with the information data in the comb type. So, in this paper, we like to study the PAPR reduction and comb type pilot assignment for the efficient channel estimation. Unlike the conventional SLM(selected mapping) method requiring the side information, our improved SLM method is to use the phase rotation sequence into information data without rotating phase of pilot. We use different pilot data according to the different phase rotation sequence. From the simulation result, it can be confirmed that when SLM method of 4 phase rotation sequence is used, PAPR is almost same to the block type method without pilot.

• The Korea Journal of Herbology
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• v.24 no.3
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• pp.59-68
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• 2009

Objectives : Bupleuri Radix (Siho) is prescribed as the root of different Bupleurum species on the pharmarcopoeia in Korea and China. Moreover, other species and varieties of the genus Bupleurum have been also distributed on the herbal market as Bupleuri Radix. However, due to the morphological similarity and frequent occurrence of intermediate forms, the correct identification of this radix is very difficult. To develop a reliable method for correct identification and improving the quality standards of official Bupleuri Radix, we analyzed sequences of the ribosomal RNA gene and internal transcribed spacer (rDNA-ITS) region. Methods : PCR amplification of rDNA-ITS region was performed using ITS1 and ITS4 primer from 6 Bupleurum species and 1 variety, B. falcatum L. (Siho), an improved breed of B. falcatum L. (Samdo-Siho), B. chinense DC. (Buk-Siho), B. scorzonerifolium Willd. (Nam-Siho), B. longiadiatum Turcz. (Gae-Siho), B. euphorbiodes Nakai (Deungdae-Siho) and B. latissimum Nakai (Seom-Siho), and nucleotide sequence was determined after sub-cloning into the pGEM-Teasy vector. Authentic marker nucleotides were estimated by the analysis of ClastalW using entire rDNA-ITS sequence of three samples per species. Results : In comparative analysis of the rDNA-ITS sequences, we found specific nucleotides to distinguish Korean (B. falcatum L. and its variety) and Chinese official species (B. chinense DC. and B. scorzonerifolium Willd.) from others at positions 411 and 447, and positions 89, 101, 415 and 599, respectively. Futhermore, we also found nucleotide indels (insertion and/or deletion) and substitutions to identify each of different Bupleurum species, 2 positions for B. falcatum L. and its variety, 6 positions for B. chinense DC., 49 positions for B. scorzonerifolium Willd., 8 positions for B. euphorbioides Nakai, 7 positions for B. longiradiatum Nakai and 9 positions for B. latissimum Nakai. These sequence differences at corresponding positions are avaliable nucleotide markers to determine the botanical origins of Bupleuri Radix. Moreover, we confirmed the phylogenetic relationship of B. latissimum Nakai, a Korean endemic speices, among Bupleurum species based on the rDNA-ITS sequence. Conclusions : These marker nucleotides would be useful to identify the official herbal medicines by the providing of definitive information that can identify each plant species and distinguish it from unauthentic adulterant Bupleurum species.

• Journal of Life Science
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• v.21 no.10
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• pp.1452-1459
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• 2011

Citrus is a common term and genus (Citrus) of flowering plants in the rue family, Rutaceae. Citrus is believed to have originated in the part of Southeast Asia bordered by Northeastern India, Myanmar (Burma) and the Yunnan province of China. The taxonomy and systematics of the genus are complex and the precise number of natural species is unclear, as many of the named species are clonally propagated hybrids, and there is genetic evidence that even some wild, true-breeding species are of a hybrid origin. One of the most popular sequences for phylogenetic inference at the generic and infrageneric levels in plants is the chloroplast trnL-trnF region. We evaluated the seven taxa with the trnL-trnF region to estimate phenotypic relationships within the genera Citrus, Poncirus, and Fortunella in Korea. Alignment of the DNA sequences required the addition of numerous gaps. Sequence variation within Citrus was mostly due to insertion/deletion. Within the genus Citrus, C. lomonia and C. sinensis were relatives and sistered with C. aurantium in the four phylogenetic analyses (MP, ML, ME, and NJ). However, some external nodes were poorly supported.