• Proceedings of the Korean Society for Bioinformatics Conference
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• 2005.09a
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• pp.147-150
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• 2005

Proper PCR primer design determines the success or failure of Polymerase Chain Reaction (PCR) reactions. In this project, we develop GENE-PRIMER, a genomes specific PCR primer design program that is amenable to a genome-wide scale. To achieve this, we incorporated various parameters with biological significance into our program, namely, primer length, melting temperature of primers Tm, guanine/cytosine (GC) content of primer, homopolymeric runs in primer and self-hybridization tendency of primer. In addition, BLAST algorithm is utilized for the purpose of primer specificity check. In summary, selected primers adhered to both physico-chemical criteria and also display specificity to intended binding site in the genome.

• The Plant Pathology Journal
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• v.34 no.3
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• pp.191-198
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• 2018

Fast and accurate diagnosis is needed to eradicate and manage economically important and invasive diseases like fire blight. Loop-mediated isothermal amplification (LAMP) is known as the best on-site diagnostic, because it is fast, highly specific to a target, and less sensitive to inhibitors in samples. In this study, LAMP assay that gives more consistent results for on-site diagnosis of fire blight than the previous developed LAMP assays was developed. Primers for new LAMP assay (named as DS-LAMP) were designed from a histidine-tRNA ligase gene (EAMY_RS32025) of E. amylovora CFBP1430 genome. The DS-LAMP amplified DNA (positive detection) only from genomic DNA of E. amylovora strains, not from either E. pyrifoliae (causing black shoot blight) or from Pseudomonas syringae pv. syringae (causing shoot blight on apple trees). The detection limit of DS-LAMP was 10 cells per LAMP reaction, equivalent to $10^4$ cells per ml of the sample extract. DS-LAMP successfully diagnosed the pathogens on four fire-blight infected apple and pear orchards. In addition, it could distinguish black shoot blight from fire blight. The $B{\ddot{u}}hlmann$-LAMP, developed previously for on-site diagnosis of fire blight, did not give consistent results for specificity to E. amylovora and on-site diagnosis; it gave positive reactions to three strains of E. pyrifoliae and two strains of P. syringae pv. syringae. It also, gave positive reactions to some healthy sample extracts. DS-LAMP, developed in this study, would give more accurate on-site diagnosis of fire blight, especially in the Republic of Korea, where fire blight and black shoot blight coexist.

• Biomolecules & Therapeutics
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• v.15 no.3
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• pp.156-161
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• 2007

Rapid advances in pharmacogenomic research have provided important information to improve drug selection, to maximize drug efficacy, and to minimize drug adverse reaction. The SNPs that are the most abundant type of genetic variants have been proven as valid biomarkers to give information on the prediction of pharmacokinetic/pharmacodynamic properties of drugs based on genotype. In order to elucidate a correlation between SNPs of calcium channel encoding gene and adverse reactions of calcium channel blockers, we investigated SNPs in CACNA1C gene known as a binding site of calcium channel blocker. 96 patients with hypertension who had taken or are taking an antihypertensive drug, 1,4-dihydropyridine (DHP) were included for analysis. These patients were composed of 47 patients with adverse drug reactions (ADR) such as edema from calcium channel blockers and 49 patients without ADR as a control group. The exons encoding the drug binding sites were amplified by PCR using specific primers, and SNPs were analyzed by direct sequencing. We found that there was no SNP in the exons encoding DHP binding site, but four novel SNPs in the exon-intron junction region. However, four novel SNPs were not associated with the ADR of calcium channel blockers. In conclusion, this study showed that ADR from calcium channel blockers may not be caused by SNPs of the binding sites of calcium channel blockers in CACNA1C gene.

• Journal of the Korean Ceramic Society
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• v.51 no.4
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• pp.278-282
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• 2014

Due to high ionic conductivity and favorable oxygen electrocatalysis, doped $Bi_2O_3$ systems are promising candidates as solid oxide fuel cell cathode materials. Recently, several researchers reported reasonably low cathode polarization resistance by adding electronically conducting materials such as (La,Sr)$MnO_3$ (LSM) or Ag to doped $Bi_2O_3$ compositions. Despite extensive research efforts toward maximizing cathode performance, however, the inherent catalytic activity and electrochemical reaction pathways of these promising materials remain largely unknown. Here, we prepare a symmetrical structure with identically sized $Y_{0.5}Bi_{1.5}O_3$/LSM composite electrodes on both sides of a YSZ electrolyte substrate. AC impedance spectroscopy (ACIS) measurements of electrochemical cells with varied cathode compositions reveal the important role of bismuth oxide phase for oxygen electrocatalysis. These observations aid in directing future research into the reaction pathways and the site-specific electrocatalytic activity as well as giving improved guidance for optimizing SOFC cathode structures with doped $Bi_2O_3$ compositions.

• Asian-Australasian Journal of Animal Sciences
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• v.12 no.5
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• pp.695-701
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• 1999

The hypothalamus is the classic site of synthesis of arginine vasotocin as neurohypophyseal hormone in the chicken. However, high concentrations of arginine vasotocin were also measured in ovarian tissues by radioimmunoassay. At first, we observed specific positive signal of mRNA encoding AVT in the hypothalamus by Northern hybridization. However, we could not find any specific bands in ovarian and uterine tissues. For evidence of transcription of the arginine vasotocin gene ingonadal tissues of the chicken, this study has applied the polymerase chain reaction as a highly sensitive assay. The hypothalamus, the four largest preovulatory ovarian follicles and the shell gland (uterus) were collected at 4 h and 20 h before oviposition. The ovarian follicular tissues were separated into granulose theca interns and theca externa layers. The uterine tissues were separated into myometrium and endometrium The extracted mRNA was converted to cDNA by reverse-transcriptase using oligo-$d(T)_{15}$ primer. Then, the cDNA was amplified by Vent polymerase and arginine vasotocin specific primers. The amplification reaction was incubated by 30 cycles successively, $95^{\circ}C$, $55^{\circ}C$ and $72^{\circ}C$ earth for 1 min. Te comparisons of the mRNA levels encoding arginine vasotocin between the tissues were determined by semi-quantification methods. After amplification of the cDNA, the PCR products were detected in hypothalamus, ovarian tissues and uterine tissues. The results of semi-quantification showed that the levels of arginine vasotocin mRNA in ovarian iud uterine tissues were about from 1/50 to 1/1000 when compared to that in the hypothalamus. The very low levels of mRNA encoding arginine vasotocin in ovarian and uterine tissues probably led us to conclude that arginine vasotocin may play a role of local mediate acting autocrine and/or paracrine.

• Macromolecular Research
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• v.16 no.1
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• pp.57-61
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• 2008

Chitosan is normally acylated and subsequently conjugated with drugs for biomedical applications. This study examined the relationship between the succinylation and gelation behaviors of glycol chitosan. Glycol chitosan was acylated with succinic anhydride under a wide variety of reaction conditions, such as different molar ratios of succinic anhydride to glucosamine, different methanol content in the reaction media, and different reaction temperatures. Among these reaction parameters, the methanol content in the solvent played an important role in determining the regioseletive succinylating site. N-succinylation and N-N cross-linking occurred regardless of the reaction conditions. However, O-succinylation was observed under specific conditions, i.e. a methanol content> 0.6 (v/v) and a reaction temperature> $25^{\circ}C$. O-succinylation accelerated the N-O cross-linking of glycol chitosan, and led to gelation. The N-succinylated glycol chitosans were water-soluble, whereas the N-and O-succinylated glycol chitosans fonned a gel. These physico-chemical structural differences in the succinylated glycol chitosans would definitely influence subsequent drug-conjugation reactions and consequently the drug loading and release kinetics.

• Journal of Soil and Groundwater Environment
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• v.25 no.1
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• pp.37-52
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• 2020

Sensitivity analysis of hydrodynamic and reaction parameters in conceptual model reflecting aquifer characteristics of Korea was performed to evaluate the uncertainty in the predicted concentrations. Among the hydrodynamic input parameters, both hydraulic conductivity (K_x) and hydraulic gradient (I) affected transport behaviors of contaminants, and resulted in same convergence concentrations with continuous injections of contaminant. However, longitudinal dispervisity (α_L) affected both transport behaviors and the convergence concentrations of contaminants. Compared to the hydrodynamic parameters, growth kinetic and degradation parameters (μ_m & K_c) more significantly affected both transport behaviors and the convergence concentrations of contaminants, indicating those parameters had higher sensitivity indices causing the uncertainties of model predictions. Considering that the sensitivity indices of both hydrodynamic and reaction parameters were a function of transport distance of groundwater, the parameters with higher sensitivity indices, a priori, need to be investigated using conceptual model reflecting site-specific aquifer characteristics before field investigation. After determining the parameters with higher sensitivity indices, the detail field investigations for the selected hydrodynamic and reaction parameters were warranted to reduce the uncertainties of model predictions.

• Korean Journal of Agricultural Science
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• v.48 no.4
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• pp.927-933
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• 2021

People have lived with and used animals for various purposes since the Paleolithic age. Therefore, animal bone research is interesting because it can infer the status of use, determine species, and ascertain the uses of animals that lived at the time. An analysis of ancient DNA was attempted to identify the species of ancient animal bones excavated from an archaeological site. Twelve animal bones from the Geumgwan Gaya period, excavated in Bonghwang-dong, Gimhae, were used in this study. After extracting DNA from the sample, polymerase chain reaction (PCR) gene amplification was performed. Species-specific primers of livestock groups such as pig, cattle, and deer were selected and used. This livestock group was a major source of protein for people who lived on the Korean Peninsula at that time. As a result, 11 sample species were identified. This study is contributes to the restoration of past life information by applying biological technologies to archaeological sites. It is also expected that such analyses of biological remains will ultimately be used to restore historical and cultural information.

• BMB Reports
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• v.32 no.5
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• pp.515-520
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• 1999

Incubation of two types of glutamate dehydrogenase isoproteins from bovine brain with the arginine-specific dicarbonyl reagent phenylglyoxal resulted in a biphasic loss of enzyme activity. Reaction of the glutamate dehydrogenase isoproteins with phenylglyoxal caused a rapid loss of 53~62% of the enzyme activities and modification of two residues of arginine per enzyme subunit. Prolonged incubation of the glutamate dehydrogenase isoproteins with phenylglyoxal resulted in the modification of an additional four residues of arginine per enzyme subunit without further loss of the residual activities. Partial protection against inactivation was provided by the coenzyme NADH or substrate 2-oxoglutarate. The most marked decrease in the rate of inactivation was observed by the combined addition of NADH and 2-oxoglutarate, suggesting that the first two modified arginine residues are in the vicinity of the catalytic site. However, inactivation of the glutamate dehydrogenase isoproteins by phenylglyoxal appears to be partial with approximately 40% activity remained after an extended reaction time with excess reagent, suggesting that the modified arginine residues may not be directly involved in catalysis. The lack of complete protection by substrates also suggest the possibility that the modified arginine residues are not directly involved at the active site, and the partial loss of activity by the modification of arginine residues may be due to a conformational change. There were no significant differences between the two glutamate dehydrogenase isoproteins in sensitivities to inactivation by phenylglyoxal, indicating that the microenvironmental structures of the glutamate dehydrogenase isoproteins are very similar to each other.

• Journal of Microbiology and Biotechnology
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• v.9 no.6
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• pp.744-750
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• 1999

Forty alcohol yeast strains were isolated from the main mashes (10 strains from each mash) for brewing of 4 different kinds of Korean traditional liquor (3 different types of Yakju and 1 Takju). Thirty-eight out of 40 strains were identified to be the same strain, Saccharomyces boulardii, by the Automated Bacteria, Yeast, and Fungi Identification System (Biolog Co., U.S.A.) based on the metabolic fingerprints. One strain that showed the highest ethanol production among the 38 strains in YPD medium, designated SHY 111, was selected and used for differentiating from other yeast type strains using the polymerase chain reaction (PCR). Amplified DNA, from transcribed internal spacers of SHY 111 chromosomal DNA, was found to be the same in both size and sequence as those of S. cerevisiae KCCM 11215 (formerly S. coreanus) and S. boulardii along with that of S. cerevisiae AB 972, which was used as a type strain for the yeast genome project. However, when PCR was carried out with the intron splice site primer, it resulted in the amplification of the SHY 111-specific DNA fragment which was about 200 bp in size. When PCR was carried out using the primer to test diversity of 40 isolated yeast strains, it was found that the PCR patterns were similar to each other except for the 200 bp bands derived from all the 10 strains from one Yakju, and 2 strains from another Yakju. These results suggest the strain identified as S. boulardii by the Automated Identification System to be a dominant strain for the fermentation of Korean traditional liquors.