• Journal of Mushroom
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• v.9 no.1
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• pp.3-16
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• 2011

In the bipolar basidiomycete Pholiota nameko, a pair of homeodomain protein genes located at the A mating-type locus regulates mating compatibility. In the present study, we used a DNA-mediated transformation system in P. nameko to investigate the homeodomain proteins that control the clamp formation. When a single homeodomain protein gene (A3-hox1 or A3-hox2) from the A3 monokaryon strain was introduced into the A4 monokaryon strain, the transformants produced many pseudo-clamps but very few clamps. When two homeodomain protein genes (A3-hox1 and A3-hox2) were transformed either separately or together into the A4 monokaryon, the ratio of clamps to the clamp-like cells in the transformants was significantly increased to approximately 50%. We, therefore, concluded that the gene dosage of homeodomain protein genes is important for clamp formation. When the sip promoter was connected to the coding region of A3-hox1 and A3-hox2 and the fused fragments were introduced into NGW19-6 (A4), the transformants achieved more than 85% clamp formation and exhibited two nuclei per cell, similar to the dikaryon (NGW12-163 ${\times}$ NGW19-6). The results of real-time RT-PCR confirmed that sip promoter activity is greater than that of the native promoter of homeodomain protein genes in P. nameko. So, we concluded that nearly 100% clamp formation requires high expression levels of homeodomain protein genes and that altered expression of the A mating-type genes alone is sufficient to drive true clamp formation.

• Molecules and Cells
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• v.26 no.1
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• pp.53-60
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• 2008

We characterized the human endogenous retrovirus (HERV-W) family in humans and primates. In silico expression data indicated that 22 complete HERV-W families from human chromosomes 1-3, 5-8, 10-12, 15, 19, and X are randomly expressed in various tissues. Quantitative real-time RT-PCR analysis of the HERV-W env gene derived from human chromosome 7q21.2 indicated predominant expression in the human placenta. Several copies of repeat sequences (SINE, LINE, LTR, simple repeat) were detected within the complete or processed pseudo HERV-W of the human, chimpanzee, and rhesus monkey. Compared to other regions (5'LTR, Gag, Gag-Pol, Env, 3'LTR), the repeat family has been mainly integrated into the region spanning the 5'LTRs of Gag (1398 bp) and Pol (3242 bp). FISH detected the HERV-W probe (fosWE1) derived from a gorilla fosmid library in the metaphase chromosomes of all primates (five hominoids, three Old World monkeys, two New World monkeys, and one prosimian), but not in Tupaia. This finding was supported by molecular clock and phylogeny data using the divergence values of the complete HERV-W LTR elements. The data suggested that the HERV-W family was integrated into the primate genome approximately 63 million years (Myr) ago, and evolved independently during the course of primate radiation.

• Journal of the Korean Data and Information Science Society
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• v.28 no.6
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• pp.1557-1564
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• 2017

We take genomic sequences of high-dimensional low sample size (HDLSS) without ordering of response categories into account. When constructing an appropriate test statistics in this model, the classical multivariate analysis of variance (MANOVA) approach might not be useful owing to very large number of parameters and very small sample size. For these reasons, we present a pseudo marginal model based upon the Gini-Simpson index estimated via Bayesian approach. In view of small sample size, we consider the permutation distribution by every possible n! (equally likely) permutation of the joined sample observations across G groups of (sizes $n_1,{\ldots}n_G$). We simulate data and apply false discovery rate (FDR) and positive false discovery rate (pFDR) with associated proposed test statistics to the data. And we also analyze real SARS data and compute FDR and pFDR. FDR and pFDR procedure along with the associated test statistics for each gene control the FDR and pFDR respectively at any level ${\alpha}$ for the set of p-values by using the exact conditional permutation theory.

• Journal of Communications and Networks
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• v.14 no.1
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• pp.10-14
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• 2012

When tag privacy is required in radio frequency identification (ID) system, a reader needs to identify, and optionally authenticate, a multitude of tags without revealing their IDs. One approach for identification with lightweight tags is that each tag performs pseudo-random function with his unique embedded key. In this case, a reader (or a back-end server) needs to perform a brute-force search for each tag-reader interaction, whose cost gets larger when the number of tags increases. In this paper, we suggest a simple and efficient identification technique that reduces readers computation to $O$(${\sqrt{N}}$ log$N$) without increasing communication cost. Our technique is based on the well-known "meet-in-the-middle" strategy used in the past to attack symmetric ciphers.

• The Plant Pathology Journal
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• v.31 no.4
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• pp.371-378
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• 2015

Surveys of yellowing viruses in plastic tunnels and in open field crops of melon (Cucumis melo cultivar catalupo), oriental melon (C. melo cultivar oriental melon), and cucumber (C. sativus) were carried out in two melon-growing areas in 2014, Korea. Severe yellowing symptoms on older leaves of melon and chlorotic spots on younger leaves of melon were observed in the plastic tunnels. The symptoms were widespread and included initial chlorotic lesions followed by yellowing of whole leaves and thickening of older leaves. RT-PCR analysis using total RNA extracted from diseased leaves did not show any synthesized products for four cucurbit-infecting viruses; Beet pseudo-yellows virus, Cucumber mosaic virus, Cucurbit yellows stunting disorder virus, and Melon necrotic spot virus. Virus identification using RT-PCR showed Cucurbit aphid-borne yellows Virus (CABYV) was largely distributed in melon, oriental melon and cucumber. This result was verified by aphid (Aphis gossypii) transmission of CABYV. The complete coat protein (CP) gene amplified from melon was cloned and sequenced. The CP gene nucleotide and the deduced amino acid sequence comparisons as well as phylogenetic tree analysis of CABYV CPs showed that the CABYV isolates were undivided into subgroups. Although the low incidence of CABYV in infections to cucurbit crops in this survey, CABYV may become an important treat for cucurbit crops in many different regions in Korea, suggesting that CABYV should be taken into account in disease control of cucurbit crops in Korea.

• Proceedings of the Korean Operations and Management Science Society Conference
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• 2001.10a
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• pp.253-256
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• 2001

Today's rapid development in the computer and network technology makes the environment which enables the companies to consider their decisions on the wide point of view and enables the software vendors to make the software packages to help these decisions. To make these software packages, many algorithms should be developed. The production and distribution planning problem belongs to those problems that industry manufacturers daily face in organizing their overall production plan. However, this combinatorial optimization problem can not be solved optimally in a reasonable time when large instances are considered. This legitimates the search for heuristic techniques. As one of these heuristic techniques, genetic algorithm has been considered in many researches. A standard genetic algorithm is a problem solving method that apply the rules of reproduction, gene crossover, and mutation to these pseudo-organisms so those organisms can Pass beneficial and survival-enhancing traits to new generation. This standard genetic algorithm should not be applied to this problem directly because when we represent the chromosome of this problem, there may exist high epitasis between genes. So in this paper, we proposed the hybrid genetic algorithm which turns out to better result than standard genetic algorithms

• Interdisciplinary Bio Central
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• v.2 no.2
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• pp.4.1-4.6
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• 2010

The most common type of microarray experiment has a simple design using microarray data obtained from two different groups or conditions. A typical method to identify differentially expressed genes (DEGs) between two conditions is the conventional Student's t-test. The t-test is based on the simple estimation of the population variance for a gene using the sample variance of its expression levels. Although empirical Bayes approach improves on the t-statistic by not giving a high rank to genes only because they have a small sample variance, the basic assumption for this is same as the ordinary t-test which is the equality of variances across experimental groups. The t-test and empirical Bayes approach suffer from low statistical power because of the assumption of normal and unimodal distributions for the microarray data analysis. We propose a method to address these problems that is robust to outliers or skewed data, while maintaining the advantages of the classical t-test or modified t-statistics. The resulting data transformation to fit the normality assumption increases the statistical power for identifying DEGs using these statistics.

• Journal of the Korean Operations Research and Management Science Society
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• v.26 no.4
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• pp.133-141
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• 2001

Rapid development in computer and network technology these days has created in environment in which decisions for manufacturing companies can be made in a much broader perspective. Especially, better decisions on production and distribution planning(PDP) problems can be made laking advantage of real time information from all the parties concerned. However, since the PDP problem-a core part of the supply chain management- is known to be the so-called NP-hard problem, so heuristic methods are dominantly used to find out solutions in a reasonable time. As one of those heuristic techniques, many previous studios considered genetic a1gorithms. A standard genetic a1gorithm applies rules of reproduction, gene crossover, and mutation to the pseudo-organisms so the organisms can pass along beneficial and survival-enhancing trails to a new generation. When it comes to representing a chromosome on the problem, it is hard to guarantee an evolution of solutions through classic a1gorithm operations alone, for there exists a strong epitasis among genes. To resolve this problem, we propose a hybrid genetic a1gorithm based on Silver-Meal heuristic. Using IMS-TB(Intelligent Manufacturing System Test-bed) problem sets. the good performance of the proposed a1gorithm is demonstrated.

• Proceedings of the Korean Society for Noise and Vibration Engineering Conference
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• 2006.05a
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• pp.187-192
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• 2006

Helicopter noise has been considered as one of major design factors like a performance and safety since the public acceptance, comfortability and stealth aspects were important for customers. According to the airworthiness regulation, the noise levels in throe different flight conditions shall comply with the specific limits. Main and tail rotors noise is most dominant in far field due to the low and mid range frequency characteristics. It is an air-born noise so That the accurate aerodynamic data is necessary for the accurate noise prediction. In KARI, low noise main and tail rotors as well as analysis codes have been developed since 2000. The approach for low noise main rotor is a kind of tip modifications, so called twin vortices tip to reduce the BVI noise. Analysis results show the 9.3dB reduction in terms of pseudo EPNL. The uneven spacing concept is applied for low noise tail rotor. Three or four decibel noise reduction is achieved by new optimized uneven spacing. Rotor noise and aerodynamic prediction codes have been improved also.

• BMB Reports
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• v.50 no.5
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• pp.235-236
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• 2017

The circadian clock is an internal system that is synchronized by external stimuli, such as light and temperature, and influences various physiological and developmental processes in living organisms. In the model plant Arabidopsis, transcriptional, translational and post-translational processes are interlocked by feedback loops among morning- and evening-phased genes. In a post-translational loop, plant-specific single-gene encoded GIGANTEA (GI) stabilize the F-box protein ZEITLUPE (ZTL), driving the targeted-proteasomal degradation of TIMING OF CAB EXPRESSION 1 (TOC1) and PSEUDO-RESPONSE REGULATOR 5 (PRR5). Inherent to this, we demonstrate the novel biochemical function of GI as a chaperone and/or co-chaperone of Heat-Shock Protein 90 (HSP90). GI prevents ZTL degradation as a chaperone and facilitates ZTL maturation together with HSP90/HSP70, enhancing ZTL activity in vitro and in planta. GI is known to be involved in a wide range of physiology and development as well as abiotic stress responses in plants, but it could also interact with diverse client proteins to increase protein maturation. Our results provide evidence that GI helps proteostasis of ZTL by acting as a chaperone and a co-chaperone of HSP90 for proper functioning of the Arabidopsis circadian clock.