• Journal of Microbiology and Biotechnology
• /
• v.18 no.7
• /
• pp.1235-1244
• /
• 2008

Indole-3-acetic acid (IAA) is produced commonly by plants and many bacteria, however, little is known about the genetic basis involving the key enzymes of IAA biosynthetic pathways from Bacillus spp. IAA intermediates from the Gram-positive spore-forming bacterium Paenibacillus polymyxa E681 were investigated, which showed the existence of only an indole-3-pyruvic acid (IPA) pathway for IAA biosynthesis from the bacterium. Four open reading frames (ORFs) encoding indole-3-pyruvate decarboxylase-like proteins and putative indole-3-pyruvate decarboxylase (IPDC), a key enzyme in the IPA synthetic pathway, were found on the genome sequence database of P. polymyxa and cloned in Escherichia coli DH5$\alpha$. One of the ORFs, PP2_01257, was assigned as probable indole-3-pyruvate decarboxylase. The ORF consisted of 1,743 nucleotides encoding 581 amino acids with a deduced molecular mass of 63,380 Da. Alignment studies of the deduced amino acid sequence of the ORF with known IPDC sequences revealed conservation of several amino acids in PP2_01257, essential for substrate and cofactor binding. Recombinant protein, gene product of the ORF PP2_01257 from P. polymyxa E681, was expressed in E. coli BL21 (DE3) as a glutathione S-transferase (GST)-fusion protein and purified to homogeneity using affinity chromatography. The molecular mass of the purified enzyme showed about 63 kDa, corresponding closely to the expected molecular mass of IPDC. The indole-3-pyruvate decarboxylase activity of the recombinant protein, detected by HPLC, using IPA substrate in the enzyme reaction confirmed the identity and functionality of the enzyme IPDC from the E681 strain.

• The Plant Pathology Journal
• /
• v.34 no.6
• /
• pp.532-543
• /
• 2018

Complete genome sequences of 22 isolates of Cucurbit aphid-borne yellows virus (CABYV), collected from melon plants showing yellowing symptom in Korea during the years 2013-2014, were determined and compared with previously reported CABYV genome sequences. The complete genomes were found to be 5,680-5,684 nucleotides in length and to encode six open reading frames (ORFs) that are separated into two regions by a non-coding internal region (IR) of 199 nucleotides. Their genomic organization is typical of the genus Polerovirus. Based on phylogenetic analyses of complete nucleotide (nt) sequences, CABYV isolates were divided into four groups: Asian, Mediterranean, Taiwanese, and R groups. The Korean CABYV isolates clustered with the Asian group with > 94% nt sequence identity. In contrast, the Korean CABYV isolates shared 87-89% sequence identities with the Mediterranean group, 88% with the Taiwanese group, 81-84% with the CABYV-R group, and 72% with another polerovirus, M.. Recombination analyses identified 24 recombination events (12 different recombination types) in the analyzed CABYV population. In the Korean CABYV isolates, four recombination types were detected from eight isolates. Two recombination types were detected in the IR and P3-P5 regions, respectively, which have been reported as hotspots for recombination of CABYV. This result suggests that recombination is an important evolutionary force in the genetic diversification of CABYV populations.

• Journal of Microbiology and Biotechnology
• /
• v.29 no.5
• /
• pp.696-703
• /
• 2019

Cronobacter sakazakii is an opportunistic pathogen causing serious infections in neonates. In this study, a bacteriophage ${\Phi}CS01$, which infects C. sakazakii, was isolated from swine feces and its morphology, growth parameters, and genomic analysis were investigated. Transmission electron microscopy revealed that ${\Phi}CS01$ has a spherical head and is 65.74 nm in diameter with a 98.75 nm contracted tail, suggesting that it belongs to the family Myoviridae. The major viral proteins are approximately 71 kDa and 64 kDa in size. The latent period of ${\Phi}CS01$ was shown to be 60 min, and the burst size was 90.7 pfu (plaque-forming units)/infected cell. Bacteriophage ${\Phi}CS01$ was stable at $4-60^{\circ}C$ for 1 h and lost infectivity after 1 h of heating at $70^{\circ}C$. Infectivity remained unaffected at pH 4-9 for 2 h, while the bacteriophage was inactivated at pH <3 or >10. The double-stranded ${\Phi}CS01$ DNA genome consists of 48,195 base pairs, with 75 predicted open reading frames. Phylogenetic analysis is closely related to that of the previously reported C. sakazakii phage ESP2949-1. The newly isolated ${\Phi}CS01$ shows infectivity in the host bacterium C. sakazakii, indicating that it may be a promising alternative to antibacterial agents for the removal of C. sakazakii from powdered infant formulas.

• Proceedings of the Korea Water Resources Association Conference
• /
• 2015.05a
• /
• pp.106-106
• /
• 2015

The information of flow regimes continues to be norm in water resource and watershed management, in that stream flow regime is a crucial factor influencing water quality, geomorphology, and the community structure of stream biota. The objectives of this study were to estimate Korean stream flows from landscape variables, classify stream flow gages using hydraulic characteristics, and then apply these methods to ungaged biological monitoring sites for effective ecological assessment. Here I used a linear modeling approach (MLR, PCA, and PCR) to describe and predict seasonal flow statistics from landscape variables. MLR models were successfully built for a range of exceedance discharges and time frames (annual, January, May, July, and October), and these models explained a high degree of the observed variation with r squares ranging from 0.555 (Q95 in January) to 0.899 (Q05 in July). In validation testing, predicted and observed exceedance discharges were all significantly correlated (p<0.01) and for most models no significant difference was found between predicted and observed values (Paired samples T-test; p>0.05). I classified Korean stream flow regimes with respect to hydraulic and hydrologic regime into four categories: flashier and higher-powered (F-HP), flashier and lower-powered (F-LP), more stable and higher-powered (S-HP), and more stable and lower-powered (S-LP). These four categories of Korean streams were related to with the characteristics of environmental variables, such as catchment size, site slope, stream order, and land use patterns. I then applied the models at 684 ungaged biological sampling sites used in the National Aquatic Ecological Monitoring Program in order to classify them with respect to basic hydrologic characteristics and similarity to the government's array of hydrologic gauging stations. Flashier-lower powered sites appeared to be relatively over-represented and more stable-higher powered sites under-represented in the bioassessment data sets.

• The Journal of Korean Institute of Information Technology
• /
• v.17 no.8
• /
• pp.1-9
• /
• 2019

With the development of imaging information communication technology in modern society, imaging acquisition and mass production technology have developed rapidly. However, crime rates using these technology are increased and forensic studies are conducted to prevent it. Identification techniques for image acquisition devices are studied a lot, but the field is limited to images. In this paper, camera model identification technique for video, not image is proposed. We analyzed video frames using the trained model with images. Through training and analysis by considering the frame characteristics of video, we showed the superiority of the model using the P frame. Then, we presented a video camera model identification system by applying a majority-based decision algorithm. In the experiment using 5 video camera models, we obtained maximum 96.18% accuracy for each frame identification and the proposed video camera model identification system achieved 100% identification rate for each camera model.

• Korean Journal of Fisheries and Aquatic Sciences
• /
• v.39 no.3
• /
• pp.261-268
• /
• 2006

Fish-frames are processing byproducts, which are left after obtaining fillets or muscle during fish processing. The fish-frame generally consists of muscle, collagen, calcium, eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA). We used fish-frame powder (FFP) of chum salmon and skipjack tuna to prepare and characterize snacks for human consumption with different proportions of FFP. The crude protein and lipid contents of fish-frames were 16.3 and 9.4% for chum salmon and 18.6 and 8.3% for skipjack tuna, respectively. The volatile basic nitrogen (30.6 mg/100 g) and browning index (0.393) of FFP from chum salmon were lower than those of FFP from skipjack tuna. Thus, the FFP of chum salmon was better for making snacks than that of skipjack tuna. Five snacks were prepared with 0, 10, 20, 30, and 40% (w/w) substitution ratios of FFP from chum salmon. The moisture content of the snacks decreased (33.6 to 11.5%) with increasing FFP substitution ratio, whereas crude ash (2.9 to 7.5%), protein (11.4 to 18.4%) and lipid (13.7 to 35.1%) increased. Sensory scores for the texture and taste of the snack with 30% FFP were significantly higher (p<0.05) than those for other snacks; the color and flavor scores of all snacks did not differ significantly. The major fatty acids in the snacks were 16:0 and 18:0 as saturates, 18:1n-9 as monoenes, and 18:2n-6 and 18:3n-3 as polyenes. Snacks with FFP contained small amounts of EPA (0.5 to 0.8%) and DHA (1.3 to 1.8%) in the total lipid composition. The total amino acid content (16.08 g/100 g) of the snack with 30% FFP was higher than that of the snack without FFP (11.18 g/100 g), and the major amino acids were aspartic acid, glutamic acid, glycine, leucine, and lysine. The calcium and phosphorus contents of the snack with 30% FFP were 1,272 mg/100 g and 854 mg/100 g, respectively, and their ratio was the optimal range (2:1 to 1:2) for body absorption efficiency.

• Korean Journal of Veterinary Research
• /
• v.38 no.4
• /
• pp.898-908
• /
• 1998

The aim of this experiments were to assess the time-interval change of motional characteristics in frozen-thawed semen of Korean native cattle (KNC) by using computer aided semen analysis (CASA) technology. Twenty-six KNC frozen semen straws were obtained from Korean KNC improvement department, livestock improvement main division, national livestock cooperatives federation in Korea. Specimens were allowed to thaw at $37^{\circ}C$ for 30 sec in water bath. Semen analysis was performed on semen image analysis system (SIAS, Medical supply, Korea) adjusted to the gate settings and used the semen droplet ($5{\mu}l$) placed on Makler counting chamber (Sefi medical instrument, Israel) prewarmed at $37^{\circ}C$. The same person used the same micropipette to fill the Makler counting chamber. A total of 150 or more of sperms were analysed in each specimen by a single trained person by scanning at least 5 to 10 fields. The measurement parameters in SIAS were as follows ; frame rate = 30 frames per sec, image capture = 1 sec, minimum motile speed = $10{\mu}m/s$, maximum countable sperm number = 400. Statistical analysis was done by Student t-test with use of the Sigma plot program on a IBM personal computer. The dancemean(DNM) and hyperactivated sperm(HYP) of frozen-thawed KNC semen kinematics were significantly decreased(p < 0.05) after 10 min of incubation at $37^{\circ}C$ water bath. But, wobble(WOB) of same sample semen was significantly increased(p < 0.05) after 10 min of incubation and significantly decrease(p < 0.05) after 60 min of same incubation. And, after 30 mim of incubation, significantly differences were found most of motion kinematics, motifity(MOT), curvilinear velocity(VCL), straight line velocity(VSL), average path velocity(VAP), amplitude of lateral head displacement(ALH), beat cross frequency(BCF), mean angular displacement(MAD), dance(DNC), on same sample semen. The DNM of KNC semen sample was variable kinematics after 30 min of incubation. Also, the linearity(LIN) and straightness(STR) was significantly decreased(p < 0.05) from 60 min of incubation. In conclusion, the AI within 30 min after thawing of frozen semen can be an effective method for obtaining high fertility rate in KNC reproductive program.

• Proceedings of the Zoological Society Korea Conference
• /
• 1998.10b
• /
• pp.113-113
• /
• 1998

In Saccharomyces cerevisiae UV irradiation and a variety of chemical DNA -damaging agents induce the transcription of specific genes, including several involved in DNA repair. One of the best characterized of DNA -damage inducible genes is PHRI, which encodes the apoenzyme for DNA photolyase. Basal-level and damage-induced expression of PHRI require an upstream activation sequence, UASPHRI. Here we report the identification of the UlvIE6 gene of S. cerevisiae as a regulator of UASPHRl activity. Surprisingly, the effect of deletion of UME6 is growth phase dependent. In wild-type cells PHRI is induced in late exponential phase, concomitant with the initiation of glycogen accumulation that precedes the diauxic shift. Deletion of UNIE6 abolishes this induction, decreases the steady-state concentration of photolyase molecules and PHRI mRNA, and increases the UV sensitivity of a rad2 mutant. The results suggest that UM E6 contributes to the regulated expression of a subset of damage-responsive genes in yeast. Furthermore, the upstream repression sequence, URSPHRI, is required for repression and damage-induced expression of PHRl. Here we show identification of YER169W and YDR096W as putative regulators acting through $URS_{PHRI}$. These open reading frames were designated as RPHI (YERl69W) and RPH2 (YDR096W) indicating regulator of PHRI. Simultaneous disruption of both genes showed a synergistic effect, producing a four-fold increase in basal level expression and a similar decrease m the induction ratio following treatment of methyl methanesulfonate(MMS). Mutation of the sequence ($AG_4$) bound by Rphlp rendered the promoter of PHRI insensitive to changes in RPHI or RPH2 status. The data suggest that RPHI and RPH2 act as damage-responsive negative regulators of PHRI. Surprisingly, the sequence bound by Rphlp in vitro is found to be $AG_4$ which is identical to the consensus binding site for the regulators Msn2p and Msn4p involved in stress-induced expression. Deletion of MSN2 and MSN4 has little effect on the induction$.$ ratio following DNA damage. However, all deletions led to a significant decrease in basal-level and induced expression of PHRI. These results imply that MSN2 and MSN4 are positive regulators of P HRI but are not required for DNA damage repression. [Supported by grant from NIH]om NIH]

• Journal of Microbiology and Biotechnology
• /
• v.17 no.9
• /
• pp.1460-1468
• /
• 2007

In this study, an approx. 2.5-kb gene fragment including the catalase gene from Rhodospirillum rubrum S1 was cloned and characterized. The determination of the complete nucleotide sequence revealed that the cloned DNA fragment was organized into three open reading frames, designated as ORF1, catalase, and ORF3 in that order. The catalase gene consisted of 1,455 nucleotides and 484 amino acids, including the initiation and stop codons, and was located 326 bp upstream in the opposite direction of ORF1. The catalase was overproduced in Escherichia coli UM255, a catalase-deficient mutant, and then purified for the biochemical characterization of the enzyme. The purified catalase had an estimated molecular mass of 189 kDa, consisting of four identical subunits of 61 kDa. The enzyme exhibited activity over a broad pH range from pH 5.0 to pH 11.0 and temperature range from $20^{\circ}C$ to $60^{\circ}C$C. The catalase activity was inhibited by 3-amino-1,2,4-triazole, cyanide, azide, and hydroxylamine. The enzyme's $K_m$ value and $V_{max}$ of the catalase for $H_2O_2$ were 21.8 mM and 39,960 U/mg, respectively. Spectrophotometric analysis revealed that the ratio of $A_{406}$ to $A_{280}$ for the catalase was 0.97, indicating the presence of a ferric component. The absorption spectrum of catalase-4 exhibited a Soret band at 406 nm, which is typical of a heme-containing catalase. Treatment of the enzyme with dithionite did not alter the spectral shape and revealed no peroxidase activity. The combined results of the gene sequence and biochemical characterization proved that the catalase cloned from strain S1 in this study was a typical monofunctional catalase, which differed from the other types of catalases found in strain S1.

• Applied Biological Chemistry
• /
• v.38 no.2
• /
• pp.111-117
• /
• 1995

In Escherichia coli, CRP forms a complex with cAMP and acts as a transcriptional regulator of many genes, including sugar metabolism operons. The E. coli MK2001, which is introduced the altered crp, is functional in the expression of lac, ara and man, in the absence of cAMP. However, the expression of mal gene is fully activated by the addition of cAMP or cGMP. The object of the study is cloning of the sfs (sugar fermentation stimulation) genes, which was involved in regulation of mal gene expression with the altered crp gene, and structural analysis and characterization of the genes at the molecular level. We have cloned 5 different E. coli genes which stimulate the maltose metabolism in a crp, cya::km (MK2001) background. Newly identified genes were designated as sfs. One of the sfs genes (pPC1), located at the 53.2 min map position on the E. coli chromosome, was further analyzed. Expression of the genes, which is involved in maltose metabolism, malQ (amylomaltase), was increased to 5.8-fold in the presence of a plasmid, pAP5, containing the subcloned sfs4 gene. The nucleotide seguence of a common 2,126 bp segment of the pPCM1 was determined and two open reading frames (ORF1 and ORF2) were detected. The ORF1 encodes the sfs4 gene and ORF2 encodes a truncated protein. Potential CRP binding site is located in the upstream of the putative promoter in the regulatory region. Expression of the cloned sfs4 gene was positively regulated by the cAMP-CRP complex.