• Journal of the Korean Data and Information Science Society
• /
• v.26 no.4
• /
• pp.813-826
• /
• 2015

This research deals with an estimation method for kinetic reaction model. The kinetic reaction model is a model to explain spread or changing process based on interaction between species on the Biochemical area. This model can be applied to a model for disease spreading as well as a model for system Biology. In the search, we assumed that the spread of species is stochastic and we construct the reaction model based on stochastic movement. We utilized Gillespie algorithm in order to construct likelihood function. We introduced a Bayesian estimation method using Markov chain Monte Carlo methods that produces more stable results. We applied the Bayesian estimation method to the Lotka-Volterra model and gene transcription model and had more stable estimation results.

• Journal of Astronomy and Space Sciences
• /
• v.28 no.4
• /
• pp.285-290
• /
• 2011

This paper presents an algorithm that can provide initial conditions for formation flying at the beginning of a region of interest to maximize scientific mission goals in the case of a tetrahedral satellite formation. The performance measure is to maximize the quality factor that affects scientific measurement performance. Several path constraints and periodicity conditions at the beginning of the region of interest are identified. The optimization problem is solved numerically using a direct transcription method. Our numerical results indicate that there exist an optimal configuration and states of a tetrahedral satellite formation. Furthermore, the initial states and algorithm presented here may be used for reconfiguration maneuvers and fuel balancing problems.

• Proceedings of the Korean Society of Plant Pathology Conference
• /
• 2003.10a
• /
• pp.143.2-143
• /
• 2003

A rapid and sensitive assay for the specific detection of plant viroids using reverse transcription-polymerase chain reaction(RT-PCR) has been developed already. The nested RT-PCR assay cloud be applied for the detection of apple scar skin viroid(ASSVd) from young leaves and other tissues. ASSVd has central conserved region(CCR), terminal left(T$\sub$L/) and terminal right(T$\sub$R/) domain. Primers were designed from these regions. Primer sets were successfully applicable for the amplification of full length or partial region of ASSVd by nested RT-PCR. Nested RT-PCR assay was more sensitive and accurate method to detect ASSVd from young trees during the early time of apple cultivation.

• Archives of Pharmacal Research
• /
• v.18 no.6
• /
• pp.376-380
• /
• 1995

Monocyte adhesion involves specific cell surface receptors, integrins and results in cell differentiation. We have studied expression and regulation of integrin .${\alpha}_5{\beta}_1$ during differntiation of U937 as in vitro model. To determine expression of integrin ${\alpha}_5{\beta}_1$ during differentiation of U937 as in vitro model. To determine expression of integrin ${\alpha}_5{\beta}_1$ genes by RT-PCR (reverse transcription and polymerase chain reaction) method. We determined expression of integrin ${\alpha}_5{\beta}_1$ genes by RT-PCE (reverse transcription and polymerase chain reaction) method. We found that expression of integrin .alpha.5.betha.1 was greatly increased during PMA-induced differentiation of U937 cells and also found that PMA-induced expression of integrin ${\alpha}_5{\beta}_1$ was inhibited by colchicine, microtubule depoly merizing agent. These results indicate that microtubular integrity is associated with expression of integrin. ${\alpha}_5{\beta}_1$ during PMA-induced differentiation of U937 cells.

• Research in Plant Disease
• /
• v.27 no.3
• /
• pp.120-127
• /
• 2021

Plant viruses cause significant yield losses, continuously compromising crop production and thus representing a serious threat to global food security. Tomato spotted wilt virus (TSWV) is the most harmful plant virus that mainly infects horticultural crops and has a wide host range. Reverse-transcription quantitative real-time PCR (RT-qPCR) has been widely used for detecting TSWV with high sensitivity, but its application is limited owing to the lack of standardization. Therefore, in this study, a sensitive and accurate reverse transcription droplet digital polymerase chain reaction (RT-ddPCR) method was established for TSWV detection. Additionally, we compared the sensitivities of RT-qPCR and RT-ddPCR for TSWV detection. Specificity analysis of RT-ddPCR for TSWV showed no amplification for main pepper viruses and negative control. TSWV transcripts levels measured by RT-ddPCR and RT-qPCR showed a high degree of linearity; however, the former yielded results that were at least 10-fold more sensitive and detected lower TSWV copy numbers than the latter. Collectively, our findings show that RT-ddPCR provides improved analytical sensitivity and specificity for TSWV detection, making it suitable for identifying low TSWV concentrations in field samples.

• Animal cells and systems
• /
• v.3 no.2
• /
• pp.181-185
• /
• 1999

Xenopus oocyte is one of the widely used heterologous expression systems of ion channels for electrophysiological studies. Here we describe a new method in which cRNA produced by polymerase chain reaction (PCR) and in vitro transcription is injected to express ion channels in oocytes. This method enables us (1) to eliminate all or a part of the untranslated region of the cDNA and to replace it with a known sequence which helps increase the expression level in oocytes, and (2) to use the PCR product for in vitro transcription without subcloning. Using this method, the expression level of one of the neuronal nicotinic acetylcholine receptors (nAChRs) $\alpha$$_{6}$ subtype in oocytes was systematically increased by more than 100-fold, which was confirmed both by the $\alpha$-Bungarotoxin ($\alpha$,/TEX>Bgt) binding assay and the current measurement.t.

• Korean Journal of Heritage: History & Science
• /
• v.54 no.1
• /
• pp.52-69
• /
• 2021

The transcriptions of Buddhist sutra in the Goryeo Dynasty are more elaborate and splendid than those of any other period and occupy a very important position in Korean bibliography. Among them, the transcriptions made on indigo paper show decorative features that represent the dignity and quality that nobles would have preferred. Particularly, during the Goryeo Dynasty, a large number of transcriptions were made on indigo paper, often in hand-scrolled and folded forms. If flexibility was not guaranteed, the hand-scrolled form caused inconvenience and damage when handling the transcription because of the structural limitations of the material that is rolled up and opened. It was possible to overcome these shortcomings by changing from the hand-scrolled to the folded form to obtain convenience and structural stability. The folded form of the transcription utilizes the same principle as the folding screen, so it is a structure that can be folded and unfolded, and it is made by connecting parts at regularly spaced intervals. No matter how small the transcription is, if it is made of thin paper, it is difficult to handle it and to maintain its shape and structure. For this reason, the folded transcription was usually made of thick paper to support the structure, and the cover was made thicker than the inner part to protect the contents. In other words, the forded form was generally manufactured to suit the characteristics of maintaining strength by making the paper thick. Because a large amount of indigo paper was needed to make this type of transcription, it is assumed that there were craftsmen who were in charge only of dark dyeing the papers. Usually, paper dyeing requires much more dye than silk dyeing, and dyeing dozens of times would be required to obtain the deep indigo color of the base of the transcription of Buddhist sutra in the Goryeo Dynasty. Unfortunately, there is no record of the Goryeo Dynasty's indigo blue paper manufacturing technique, and the craftsmen who made indigo paper no longer remain, so no one knows the exact method of making indigo paper. Recently, Hanji artisans, natural dyers, and conservators attempted to restore the Goryeo Dynasty's indigo paper, but the texture and deep colors found in the relics could not be reproduced. This study introduces the process of restoring indigo paper in the Goryeo Dynasty through collaboration between dyeing artisans, Hanji artisans, and conservators for conservation of the transcription of Buddhist sutra in the late Goryeo dynasty, yielding a suggested method of making indigo paper.

• Radiation Oncology Journal
• /
• v.17 no.4
• /
• pp.299-306
• /
• 1999

Purpose : The human genetic disorder ataxia-telangiectasia (AT) is a multisystem disease characterized by extreme radiosensitivity. The recent identification of the gene mutated in AT, ATM, and the demonstration that it encodes a homologous domain of phosphatidylinositol 3-kinase (PI3-K), the catalytic subunit of an enzyme involved in transmitting signals from the cell surface to the nucleus, provide support for a role of this gene in signal transduction. Although ionizing radiation was known to induce c-fos transcription, nothing is known about how ATM or PKCI mediated signal transduction pathway modulates the c-fos gene transcription and gene expression. Here we have studied the effect of PKCI on radiation sensitivity and c-fos transcription in normal and AT cells. Materials and Methods: Normal (LM217) and AT (AT5BIVA) cells were transfected with PKCI expression plasmid and the overexpression and integration of PKCI was evaluated by northern blotting and polymerase chain reaction, respectively. 5 Gy of radiation was exposed to LM and AT cells transfected with PKCI expression plasmid and cells were harvested 48 hours after radiation and investigated apoptosis with TUNEL method. The c-fos transcription activity was studied by performing CAT assay of reporter gene after transfection of c-fos CAT plasmid into AT and LM cells. Results: Our results demonstrate for the first time a role of PKCI on the radiation sensitivity and c-fos expression in LM and AT cells. PKCI increased radiation induced apoptosis in LM cells but reduced apoptosis in AT cells. The basal c-fos transcription activity is 70 times lower in AT cells than that in LM cells. The c-fos transcription activity was repressed by overexpression of PKCI in LM cells but not in AT cells. After induction of c-fos by Ras protein, overexpression of PKCI repressed c-fos transcription in LM cells but not in AT cells Conclusion: Overexpression of PKCI increased radiation sensitivity and repressed c-fos transcription in LM cells but not in AT cells. The results may be a. reason of increased radiation sensitivity of AT cells. PKCI may be involved in an ionizing radiation induced signal transduction pathway responsible for radiation sensitivity and c-fos transcription. The data also provided evidence for novel transcriptional difference between LM and AT cells.

• Genomics & Informatics
• /
• v.5 no.1
• /
• pp.10-18
• /
• 2007

Numerous studies have reported that genes with similar expression patterns are co-regulated. From gene expression data, we have assumed that genes having similar expression pattern would share similar transcription factor binding sites (TFBSs). These function as the binding regions for transcription factors (TFs) and thereby regulate gene expression. In this context, various analysis tools have been developed. However, they have shortcomings in the combined analysis of expression patterns and significant TFBSs and in the functional analysis of target genes of significantly overrepresented putative regulators. In this study, we present a web-based A Functional Clustering Analysis Tool for Predicted Transcription Regulatory Elements and Gene Ontology Terms (FCAnalyzer). This system integrates microarray clustering data with similar expression patterns, and TFBS data in each cluster. FCAnalyzer is designed to perform two independent clustering procedures. The first process clusters gene expression profiles using the K-means clustering method, and the second process clusters predicted TFBSs in the upstream region of previously clustered genes using the hierarchical biclustering method for simultaneous grouping of genes and samples. This system offers retrieved information for predicted TFBSs in each cluster using $Match^{TM}$ in the TRANSFAC database. We used gene ontology term analysis for functional annotation of genes in the same cluster. We also provide the user with a combinatorial TFBS analysis of TFBS pairs. The enrichment of TFBS analysis and GO term analysis is statistically by the calculation of P values based on Fisher’s exact test, hypergeometric distribution and Bonferroni correction. FCAnalyzer is a web-based, user-friendly functional clustering analysis system that facilitates the transcriptional regulatory analysis of co-expressed genes. This system presents the analyses of clustered genes, significant TFBSs, significantly enriched TFBS combinations, their target genes and TFBS-TF pairs.

• Journal of Microbiology and Biotechnology
• /
• v.28 no.2
• /
• pp.210-217
• /
• 2018

A one-step multiplex reverse transcription PCR (RT-PCR) method comprising six primer sets (for the detection of norovirus GI and GII, hepatitis A virus, rotavirus, and astrovirus) was developed to simultaneously detect four kinds of pathogenic viruses. The size of the PCR products for norovirus GI and GII, hepatitis A virus (VP3/VP1 and P2A regions), rotavirus, and astrovirus were 330, 164, 244, 198, 629, and 449 bp, respectively. The RT-PCR with the six primer sets showed specificity for the pathogenic viruses. The detection limit of the developed multiplex RT-PCR, as evaluated using serially diluted viral RNAs, was comparable to that of one-step single RT-PCR. Moreover, this multiplex RT-PCR was evaluated using food samples such as water, oysters, lettuce, and vegetable product. These food samples were artificially spiked with the four kinds of viruses in diverse combinations, and the spiked viruses in all food samples were detected successfully.