• Journal of Life Science
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• v.9 no.5
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• pp.556-563
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• 1999

Presence of antibody to the capsid protein p24 is the main diagnostic criterion, since this reflects reliable antibody response to HIV infection. However, it takes about 6-8 weeks for antibody production after infection and people who are infected but antibodies are not produced yet are classified as seronegative. Therefore, there is a strong need for an improved diagnostic method for better health security. As a first step for developing such an improved diagnostic system, gag protein of human immunodificiency virus type 1 was expressed in E. coli DH5$\alpha$. The gag fragment of HIV-1 (including a portion of p17 and whole p24) was amplified by polymerase chain reaction (PCR) and BamH I/EcoR I sites were created during PCR. The amplified DNA fragment was cleaved with BamH I/EcoR I and was subcloned into the GEX-2T vector which had been digested with BamHI/EcoRI, resulting gene fusion with gst gene of pGEX-2T. The recombinant DNA was transferred into E. coli DH5$\alpha$. The transformed bacteria were grown at 37$^{\circ}C$ for 3h and protein expression was induced with 0.1mM IPTG at $25^{\circ}C$ for 3h. Recombinant gag protein or GST-gag fusion protein was purified with glutathione-sepharose 4B bead and migrated as a single band when analyzed by 10% polyacrylamide gel. These proteins were confirmed by immunoblotting with anti-GST goat sera or Korean AIDS patients sera. The results of this study establish the expression and single step pulification of HIV-1 gag protein which can specifically bind with Korean AIDS patients sera.

• Journal of Microbiology and Biotechnology
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• v.11 no.3
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• pp.508-514
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• 2001

A stuructural gene (ycl) encoding novel yeast cell wall hydrolase, YCL, was cloned from alkalophilic Bacillus alcalophilus subsp. YB380 by PCR, and transformed into E. coli JM83. Based on the N-terminal and internal amino acid sequences of the enzyme, primers were designed for PCr. The positive clone that harbors 1.8 kb of the yeast cell wall hydrolase gene was selected by the colony hybridization method with a PCR fragment as a probe. According to the computer analysis, this gene contained a 400-base-paired N-terminal domain of the enzyme. Based on nucletide homology of the cloned gene, a 850 bp fragment was amplified and the C-terminal domain of the enzyme was sequenced. With a combination of the two sequences, a full nucleotide sequence for YCL was obtained. This gene, ycl, consisted of 1,297 nucleotides with 27 nucleotides with 27 amino acids of signal sequence, 83 redundant amino acids of prosequence, and 265 amino acids of the mature protein. This gene was then cloned into the pJH27 shuttle vector and transformed into the Bacillus subtilis DB104 to express the enzyme. It was confirmed that the expressed cell wall hydrolase that was produced by Bacillus subtilis DB104 was the same as that of the donor strain, by Western blot using polyclonal antibody (IgY) prepared from White Leghorn hen. Purified yeast cell wall hydrolase and expressed recombinant protein showed a single band at the same position in the Western blot analysis.

• Journal of the korean academy of Pediatric Dentistry
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• v.25 no.2
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• pp.292-303
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• 1998

The arbitrary primer polymerase chain reaction(AP-PCR) and Southern blot restriction fragment length polymorphism(RFLP) were used to genotype the cariogenic pathogen S. mutans in children. Following the morphologic chracteristics of colony on selective medium for S. mutans, total genomic DNA from 155 strains was extracted by conventional methods. Among 155 strains, 143 strains (92.3%) were confirmed S. mutans by PCR with dexA gene and 114 strains were used in this study. Three random sequence 10-base oligonucleotide primers were chosen for AP-PCR. The amplified DNA products were separated electrophoretically in a 2% agarose gel containing ethidium bromide and the banding patterns were compared among different strains. For RFLP analysis, DNA was digested with EcoRI and BamHI, separated on a 0.7 % agarose gel and transferred to a nylon membrane. The membrane was probed with a previously characterised 1.6 kilobases (kb) DNA fragment cloned from gtf B gene of S. mutans. The probe was labeled with isotope[$^{32}P-{\alpha}CTP$], and hybridized fragments were detected with intensifying screen. AP-PCR produced 4-8 DNA bands in the 0.25-10 kb regions and distinguished 9, 10 or 12 genotypes, depending on the specific primer used. Southern blot RFLP analysis revealed 2 hybridization patterns consisting of 1 DNA fragments 450, 500 bp. These results indicate that AP-PCR is more discriminative method for genotyping of S. mutans.

• The Journal of Korean Institute of Communications and Information Sciences
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• v.34 no.9A
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• pp.712-718
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• 2009

This paper proposes the optimal transmission parameter selection method for an energy efficient Wireless Personal Area Network (WPAN) system which is applicable to the Maritime Telematics targeting for various ship models. Since the transmission parameter selection is an important factor for WPAN system to decide its energy efficiency, we propose an energy consumption model for ship area network (SAN) employing IEEE 802.15.3 based TDMA HR-WPAN model and analyzes the effect of transmission parameter selection on the performance of energy consumption. In particular, the main performance decision parameter of the SAN applying HR-WPAN is path loss, since it is very varied according to the material of shipbuilding such as steel (large ship), FRP (medium size ship) and compound wood (small ship). Thus, we analyzed and demonstrated that the proper transmission parameter selection among transmit power, PHY data rate and fragment size for each ship model guarantee the energy efficiency.

• Korean Journal of Plant Taxonomy
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• v.45 no.1
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• pp.29-35
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• 2015

Sasa borealis (Hack.) Makino & Shibata is widely distributed in South Korea. With amplified fragment length polymorphism (AFLP) markers, we analyzed the genetic diversity of S. borealis to predict and measure the phytogeographical factors of these populations. Relatively high levels of genetic diversity (PPL = 37.2%, h = 0.143, I = 0.205) and genetic differentiation ($G_{ST}$ = 0.324, ${\theta}^B$ = 0.395) were confirmed in populations of S. borealis. Moreover, an analysis of molecular variance (AMOVA) showed that the rate of differentiation among the populations was 47.7%. The results showed that genetic diversity is inversely proportional to the latitude of the S. borealis populations, indicating that the distribution of S. borealis may have extended from lower to higher latitudes. This method of investigating the correlation between genetic diversity and latitude presents critical information for estimating changes in distributions and plant conservation due to climate change.

• Korean Journal of Veterinary Service
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• v.30 no.3
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• pp.393-406
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• 2007

Bovine tuberculosis is an important zoonosis worldwide. Mycobacterium bovis, the causative agent of this disease in cattle, is also a pathogen for humans and several economically important animals. The cases of tuberculosis are reported in two cow found at slaughter house located in Gwangju city. Histopathologically, in the lymph nodes, granulomas consisted of large areas of necrosis surrounded by variable thick bands of cellular infiltrate containing macrophages, Langhans-type multinucleated giant cells and lymphocytes. Lesions in the lung followed the same developmental pattern as did lesions in the lymph nodes with some exceptions. With the acid-fast staining, numerous mycobacteria were revealed in the lung and lymph nodes. M bovis was confirmed as a causative agent in these cattle using bacterial isolation and PCR and restriction fragment length polymorphism method based on a unique 12.7 kb fragment insertion sequence from the Mycobacterium tuberculosis genome and the pncA polymorphism, The insertion element IS6110 and IS1081 were present M bovis isolated from lungs and lymph nodes of cattle using PCR assay. These cases are interesting and important in public health aspect that M bovis-infected cattle were found during a routine post-mortem inspection at slaughter house.

• Biotechnology and Bioprocess Engineering:BBE
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• v.11 no.6
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• pp.510-515
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• 2006

The putative EPA synthesis gene cluster was mined from the entire genome sequence of Shewanella oneidensis MR-1. The gene cluster encodes a PKS-like pathway that consists of six open reading frames (ORFs): ORFSO1602 (multi-domain beta-ketoacyl synthase, KS-MAT-4ACPs-KR), ORFSO1600 (acyl transferase, AT), ORFSO1599 (multi-domain beta-ketoacyl synthase, KS-CLF-DH-DH), ORFSO1597 (enoyl reductase, ER), ORFSO1604 (phosphopentetheine transferase, PPT), and ORFSO1603 (transcriptional regulator). In order to prove involvement of the PKS-like machinery in EPA synthesis, a 20.195-kb DNA fragment containing the genes was amplified from S. oneidensis MR-1 by the long-PCR method. Its identity was confirmed by the methods of restriction enzyme site mapping and nested PCR of internal genes orfSO1597 and orfSO1604. The DNA fragment was cloned into Escherichia coli using cosmid vector SuperCos1 to form pCosEPA. Synthesis of EPA was observed in four E. coli clones harboring pCosEPA, of which the maximum yield was 0.689% of the total fatty acids in a clone designated 9704-23. The production yield of EPA in the E. coli clone was affected by cultivation temperature, showing maximum yield at $20^{\circ}C$ and no production at $30^{\circ}C$ or higher. In addition, production yield was inversely proportional to glucose concentration of the cultivation medium. From the above results, it was concluded that the PKS-like modules catalyze the synthesis of EPA. The synthetic process appears to be subject to regulatory mechanisms triggered by various environmental factors. This most likely occurs via the control of gene expression, protein stability, or enzyme activity.

• The Journal of Korean Institute of Communications and Information Sciences
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• v.34 no.10A
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• pp.769-775
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• 2009

This paper proposes the optimal transmission parameter selection method for an energy efficient Wireless Personal Area Network (WPAN) system which is applicable to the Maritime Telematics targeting for various ship models. Since the transmission parameter selection is an important factor for WPAN system to decide its energy efficiency, we propose an energy consumption model for ship area network (SAN) employing IEEE 802.15.3 based TDMA HR-WPAN model and analyzes the effect of transmission parameter selection on the performance of energy consumption. In particular, the main performance decision parameter of the SAN applying HR-WPAN is path loss, since it is very varied according to the material of shipbuilding such as steel (large ship), FRP (medium size ship) and compound wood (small ship). Thus, we analyzed and demonstrated that the proper transmission parameter selection among transmit power, PHY data rate and fragment size for each ship model guarantee the energy efficiency.

• Molecules and Cells
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• v.42 no.11
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• pp.783-793
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• 2019

When endoplasmic reticulum (ER) functions are perturbed, the ER induces several signaling pathways called unfolded protein response to reestablish ER homeostasis through three ER transmembrane proteins: inositol-requiring enzyme 1 (IRE1), PKR-like ER kinase (PERK), and activating transcription factor 6 (ATF6). Although it is important to measure the activity of ATF6 that can indicate the status of the ER, no specific cell-based reporter assay is currently available. Here, we report a new cell-based method for monitoring ER stress based on the cleavage of $ATF6{\alpha}$ by sequential actions of proteases at the Golgi apparatus during ER stress. A new expressing vector was constructed by using fusion gene of GAL4 DNA binding domain (GAL4DBD) and activation domain derived from herpes simplex virus VP16 protein (VP16AD) followed by a human $ATF6{\alpha}$ N-terminal deletion variant. During ER stress, the GAL4DBD-VP16AD(GV)-$hATF6{\alpha}$ deletion variant was cleaved to liberate active transcription activator encompassing GV-$hATF6{\alpha}$ fragment which could translocate into the nucleus. The translocated GV-$hATF6{\alpha}$ fragment strongly induced the expression of firefly luciferase in HeLa Luciferase Reporter cell line containing a stably integrated 5X GAL4 site-luciferase gene. The established double stable reporter cell line HLR-GV-$hATF6{\alpha}$(333) represents an innovative tool to investigate regulated intramembrane proteolysis of $ATF6{\alpha}$. It can substitute active pATF6(N) binding motif-based reporter cell lines.

• ETRI Journal
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• v.38 no.3
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• pp.518-528
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• 2016

The searching of an extensive document database for documents that are locally similar to a given query document, and the subsequent detection of similar regions between such documents, is considered as an essential task in the fields of information retrieval and data management. In this paper, we present a framework for such a task. The proposed framework employs the method of short-read mapping, which is used in bioinformatics to reveal similarities between genomic sequences. In this paper, documents are considered biological objects; consequently, edit operations between locally similar documents are viewed as an evolutionary process. Accordingly, we are able to apply the method of evolution tracing in the detection of similar regions between documents. In addition, we propose heuristic methods to address issues associated with the different stages of the proposed framework, for example, a frequency-based fragment ordering method and a locality-aware interval aggregation method. Extensive experiments covering various scenarios related to the search of an extensive document database for documents that are locally similar to a given query document are considered, and the results indicate that the proposed framework outperforms existing methods.