• Journal of Microbiology and Biotechnology
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• 제24권11호
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• pp.1503-1509
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• 2014

With the purpose of facilitating the process of stable strain generation, a shuttle vector for integration of genes via a double recombination event into two ectopic sites on the Sulfolobus acidocaldarius chromosome was constructed. The novel chromosomal integration and expression vector pINEX contains a pyrE gene from S. solfataricus P2 ($pyrE_{sso}$) as an auxotrophic selection marker, a multiple cloning site with histidine tag, the internal sequences of malE and malG for homologous recombination, and the entire region of pGEM-T vector, except for the multiple cloning region, for propagation in E. coli. For stable expression of the target gene, an ${\alpha}$-glucosidase-producing strain of S. acidocaldarius was generated employing this vector. The malA gene (saci_1160) encoding an ${\alpha}$-glucosidase from S. acidocaldarius fused with the glutamate dehydrogenase ($gdhA_{saci}$) promoter and leader sequence was ligated to pINEX to generate pINEX_malA. Using the "pop-in" and "pop-out" method, the malA gene was inserted into the genome of MR31 and correct insertion was verified by colony PCR and sequencing. This strain was grown in YT medium without uracil and purified by His-tag affinity chromatography. The ${\alpha}$-glucosidase activity was confirmed by the hydrolysis of $pNP{\alpha}G$. The pINEX vector should be applicable in delineating gene functions in this organism.

• Journal of Microbiology and Biotechnology
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• 제17권2호
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• pp.287-296
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• 2007

A Lactobacillus paraplantarum strain producing a bacteriocin was isolated from kimchi using the spot-on-the lawn method and named L. paraplantarum C7 [15]. The bacteriocin, paraplantaricin C7, was found to inhibit certain Lactobacillus strains, including L. plantarum, L. pentosus, and L. delbrueckii subsp. lactis. It also inhibited Enterococcus faecalis, yet did not inhibit most of the other LAB (lactic acid bacteria) tested. The maximum level of paraplantaricin C7 activity was observed under the culture conditions of $25^{\circ}C$ and a constant pH of 4.5. Paraplantaricin C7 retained 90% of its activity after 10 min of treatment at $100^{\circ}C$ and remained stable within a pH range of 2-8. Based on a culture supernatant, paraplantaricin C7 was purified by DEAE-Sephacel column chromatography and $C_{18}$ reverse-phase HPLC. SDS-PAGE and activity staining were then conducted using the purified paraplantaricin C7, and its molecular mass determined to be about 3,800 Da. The 28 N-terminal amino acids from the purified paraplantaricin C7 were determined, and the structural gene encoding paraplantaricin C7, ppnC7, was cloned by PCR using degenerate primers based on the N-terminal amino acid sequence. The nucleotide sequences for ppnC7 and other neighboring orfs exhibited a limited homology to the previously reported plantaricin operon genes. Paraplantaricin C7 is a novel type II bacteriocin containing a double glycine leader sequence.

• Mycobiology
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• 제44권4호
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• pp.283-290
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• 2016

A double-stranded RNA (dsRNA) mycovirus was detected in malformed fruiting bodies of Pleurotus ostreatus strain ASI2792, one of bottle cultivated commercial strains of the edible oyster mushroom. The partial RNA-dependent RNA polymerase (RdRp) gene of the P. ostreatus ASI2792 mycovirus (PoV-ASI2792) was cloned, and a cDNA sequences alignment revealed that the sequence was identical to the RdRp gene of a known PoSV found in the P. ostreatus strain. To investigate the symptoms of PoV-ASI2792 infection by comparing the isogenic virus-free P. ostreatus strains with a virus-infected strain, isogenic virus-cured P. ostreatus strains were obtained by the mycelial fragmentation method for virus curing. The absence of virus was verified with gel electrophoresis after dsRNA-specific virus purification and Northern blot analysis using a partial RdRp cDNA of PoV-ASI2792. The growth rate and mycelial dry weight of virus-infected P. ostreatus strain with PoV-ASI2792 mycovirus were compared to those of three virus-free isogenic strains on 10 different media. The virus-cured strains showed distinctly higher mycelial growth rates and dry weights on all kinds of experimental culture media, with at least a 2.2-fold higher mycelial growth rate on mushroom complete media (MCM) and Hamada media, and a 2.7-fold higher mycelial dry weight on MCM and yeast-malt-glucose agar media than those of the virus-infected strain. These results suggest that the infection of PoV mycovirus has a deleterious effect on the vegetative growth of P. ostreatus.

• Journal of fish pathology
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• 제23권2호
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• pp.177-187
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• 2010

The Interferon stimulated gene 15 (ISG15) is strongly induced in many cell types by IFNs, viral infections, and double-stranded RNA (poly I:C). The ISG15 homologue cDNA was isolated from the rock bream LPS stimulated leukocyte cDNA library. The rock bream ISG15 homologue was found to consist of 833 bp encoding 157 amino acid residues. Compared with other known ISG15 peptide sequences, the most conserved regions of the rock bream ISG15 peptide were found to be the tandem ubiquitin-like domains and a C-terminal LRLRGG conjugating motif, characteristic of mammalian and non-mammalian ISG15 proteins. Phylogenetic analysis based on the deduced amino acid sequence revealed a homologous relationship between the ISG15 sequence of rock bream and that of Atlantic salmon, Atlantic cod, northern snake head, black rockfish and olive flounder. The expression of the rock bream ISG15 molecule was induced in the peripheral blood leukocytes (PBLs) from 1 to 24 h following poly I:C stimulation, with a peak at 3 h post-stimulation. The rock bream ISG15 gene was predominantly expressed in the PBLs, spleen and gill.

• Journal of the Korea Institute of Information and Communication Engineering
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• 제13권4호
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• pp.805-812
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• 2009

In many intrusion detection applications, n-gram approach has been widely applied. However, n-gram approach has shown a few problems including unscalability and double counting of features. To address those problems, we applied n-gram augmented Naive Bayes with k-truncated suffix tree (k-TST) storage mechanism directly to classify intrusive sequences and compared performance with those of Naive Bayes and Support Vector Machines (SVM) with n-gram features by the experiments on host-based intrusion detection benchmark data sets. Experimental results on the University of New Mexico (UNM) benchmark data sets show that the n-gram augmented method, which solves the problem of independence violation that happens when n-gram features are directly applied to Naive Bayes (i.e. Naive Bayes with n-gram features), yields intrusion detectors with higher accuracy than those from Naive Bayes with n-gram features and shows comparable accuracy to those from SVM with n-gram features. For the scalable and efficient counting of n-gram features, we use k-truncated suffix tree mechanism for storing n-gram features. With the k-truncated suffix tree storage mechanism, we tested the performance of the classifiers up to 20-gram, which illustrates the scalability and accuracy of n-gram augmented Naive Bayes with k-truncated suffix tree storage mechanism.

• Journal of Microbiology and Biotechnology
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• 제25권1호
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• pp.98-108
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• 2015

Staphylococcus aureus is an important foodborne pathogen that causes diverse diseases ranging from minor infections to life-threatening conditions in humans and animals. To further understand its pathogenesis, the genome of the strain S. aureus FORC_001 was isolated from a contaminated food. Its genome consists of 2,886,017 bp double-stranded DNA with a GC content of 32.8%. It is predicted to contain 2,728 open reading frames, 57 tRNAs, and 6 rRNA operons, including 1 additional 5S rRNA gene. Comparative phylogenetic tree analysis of 40 complete S. aureus genome sequences using average nucleotide identity (ANI) revealed that strain FORC_001 belonged to Group I. The closest phylogenetic match was S. aureus MRSA252, according to a whole-genome ANI (99.87%), suggesting that they might share a common ancestor. Comparative genome analysis of FORC_001 and MRSA252 revealed two non-homologous regions: Regions I and II. The presence of various antibiotic resistance genes, including the SCCmec cluster in Region I of MRSA252, suggests that this strain might have acquired the SCCmec cluster to adapt to specific environments containing methicillin. Region II of both genomes contains prophage regions but their DNA sequence identity is very low, suggesting that the prophages might differ. This is the first report of the complete genome sequence of S. aureus isolated from a real foodborne outbreak in South Korea. This report would be helpful to extend our understanding about the genome, general characteristics, and virulence factors of S. aureus for further studies of pathogenesis, rapid detection, and epidemiological investigation in foodborne outbreak.

• Korean Journal of Applied Biomechanics
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• 제17권4호
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• pp.115-125
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• 2007

Grould Reaction force(GRF) is important in human movements and GRF measurements are one of the most frequently used tool in biomechanical studies. In the studies of the golf swing motion, people refer to GRF as weight transfer. A successful golf swing motion requires many segments activation sequences which are controled by the nerve system. Due to the inter- and intra-individual variability of the human movement and the movement strategies, reliability of the measurements are important in human movement studies. Previous golf researches were based on group studies and certain events' values were analyzed. The purposes of this study were to determine the number of trials for the reliable golf swing GRF data collection, to reveal the variability level of the meaningful components of the golf swing GRF, and to classify the types of the golf swing GRF patterns. Twenty three male professional golfers($26.4{\pm}6.6$ years, $174.3{\pm}5.2\;cm$, $71.3{\pm}6.5\;kg$) signed an informed consent form prior to participation in this study. GRFs of driver swings were collected with Kistler 9285 force platform and 9865A amplifier, and calculated by the KwonGRF program(Visol, Korea). Sampling frequency was 1080 Hz. GRF data were trimmed from 1.5 s prior to the impact to 0.5 s after the impact. The number of trials for the reliable GRF collection was determined when the change in floating mean overs the 25 % of the standard deviation of that variable. Variabilities of the variables were determined by the coefficient of variation(CV) of 10 %. The types of GRF patterns were determined by visual inspection of the peak GRF shapes. The minimum number of trials for the reliable golf swing GRF data collection was five. Ten-trial seems more conservative. The value of the peak GRF was more reliable than the value of the impact GRF. The CV of the peak GRF and impact GRF were 7.4 %, 15.2 %, respectively. Because of the +/- sigh of the peak GRF appearance time, it was impossible to calculate CV of the peak GRF appearance time. Golf swing GRF patterns were classified as sing peak type, double peak type, and plateau peak type. This classification suggests the presence of the different golf swing weight transfer strategies.

• The Journal of Korean Society of Virology
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• 제28권3호
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• pp.275-285
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• 1998

Based on the geographic range and distribution of its rodent reservoir host, the European common vole (Microtus arvalis), Tula virus is likely to be widespread throughout Eurasia. Tula virus-infected voles have been captured in Central Russia, Austria, Czech and Slovak Republics, and the former Yugoslavia. Although serologic evidence for Hantaan (HTN) or Seoul (SEO) virus infection can be found in the vast majority of the more than 300 cases of hemorrhagic fever with renal syndrome (HFRS) occurring annually in Korea, approximately 4% of Korean patients with HFRS show a more than 4-fold higher antibody titer to Puumala (PUU) virus than to HTN or SEO virus by double-sandwich IgM ELISA, suggesting the existence of pathogenic Puumala-related hantaviruses in Korea. To further define the geographic distribution and genetic diversity of Tula virus in Eurasia and to investigate the existence of previously unrecognized Microtus-borne hantavirus in Korea, arvicolid rodents were captured in Lodz, Poland in 1995 and in Yunchon-kun, Kyungki-do during April to May, 1998. In addition, sera from 18 Korean HFRS patients who showed higher (or the same) antibody titer to Tula virus than HTN and SEO viruses were examined for hantavirus RNA by RT-PCR. Hantaviral sequences were not detected in any of the 18 patients or in 35 reed voles (Microtus fortis) in Korea. Alignment and comparison of a 208-nucleotide region of the S segment, amplified from lung tissues of two hantavirus-seropositive Marvalis captured in Poland, revealed $80.8{\sim}83.2%$ sequence similarity, respectively, with Tula virus strains from Central Russia and the Czech and Slovak Republics. Phylogenetic analysis indicated that the newfound Tula virus strains from Poland were closely related to other Tula hantaviruses from Eurasia.

• Journal of Animal Science and Technology
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• 제46권4호
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• pp.547-554
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• 2004

Telomeres are nucleoprotein structures at the ends of chromosomes consisting of tandem repeat sequences of . (TTAGGG)n. Telomeres serve as guardians of the genome, protect individual chromosomes within the nucleus, and help in meiotic pairing of homologous chromosomes. To investigate the telomere distributions of cattle and pig chromosomes, fluorescence in situ hybridization(FISH) was carried out on metaphase spreads of in vitro fibroblast cultures from Holstein and Landrace using a human telomeric DNA repeat probe. Results indicate that the distinct double spots on both ends of chromosomes of cattle and pigs were observed. In cattle, there was a random variation in the intensity of telomere signals among chromosomes. In pigs, an interstitial telomeric signal was observed on the chromosome 6q1 of all the cells examined. According to quantitative fluorescence in situ hybridization(Q-FISH) analysis, some chromosomes had consistently much more telorneres at one end of chromosomes. In general, both species had consistently much more telomeres at q-end than p-end on most of chromosomes. The relative amount of telomeres on bovine chromosomes was higher than that on pig chromosomes. In additions, Y chromosome had the highest relative amount of telorneres in cattle and pigs.

• Journal of the Korea Concrete Institute
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• 제23권6호
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• pp.773-780
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• 2011

In this study, thermal stress analysis are carried out considering material properties, curing condition, ambient temperature, and casting date of the mass concrete placed in bottom slab and side wall of the in-ground type LNG tank as a super massive structure. Also, based on the numerical results, cracking possibility is predicted and counter measures to prevent the cracking are proposed. For the tasks, two optimum mix proportions were selected. From the results of the thermal stress analysis, the through crack index of 1.2 was satisfied for separately caste concrete lots except for the bottom slab caste in 2 separate sequences. For the double caste bottom slab, it is necessary introduce counter measures such as pre-cooling prior to the site construction. Also, another crack preventive measure is to lower the initial casting temperature by $25^{\circ}C$ or less to satisfy 1.2 through crack index criterion. In the $1^{st}$ and $2^{nd}$ caste bottom slab, the surface crack index was over 1.2. Therefore, the surface cracks can be controlled by implementing the curing conditions proposed in this study. Since the side wall's surface crack index was over 1.0, it is safe to assume that the counter preventive measures can control width and number of cracks.