• Korean journal of applied entomology
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• v.52 no.4
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• pp.295-304
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• 2013

This study aimed to understand the physiological status of the beet armyworm, Spodoptera exigua at low developmental threshold temperature (LTT) through analysis of gene-expression patterns associated with different functions (metabolism, nervous system, immune, and stress). The estimated LTTs for egg, larval, and pupal developments varied with $5.5{\sim}11.6^{\circ}C$. Larvae were able to develop at the lower temperatures than eggs and pupae. However, the physiological LTT ($15^{\circ}C$) in the fifth instar was much higher than the estimated LTT ($10.3^{\circ}C$). Gene expression patterns estimated by a quantitative RT-PCR (qRT-PCR) indicate that most genes in different functional groups increased their expressions with increase of larval instars. In the same fifth instar, as the treatment temperatures increased, the gene expression levels increased. Moreover, the newly molted fifth instar larvae were different in their gene expression rates according to their previous culturing temperatures. Most gene expressions were suppressed in the fifth instar larvae at the physiological LTT ($15^{\circ}C$). However, the larvae at $15^{\circ}C$ gradually exhibited significant increase in the gene expression rates with rearing time just like those at the higher temperature. These results suggest that S. exigua at LTT exhibits a typical gene expression pattern with maintaining significantly suppressed levels.

• BMB Reports
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• v.38 no.2
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• pp.167-176
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• 2005

Nuclear factor-E2-related factor 2 (Nrf2) is known as a key regulator of ARE-mediated gene expression and the induction of Phase II detoxifying enzymes and antioxidant enzymes, which is also a common property of many chemopreventive agents. In the present study, we investigated the regulatory role of different chemopreventive agents including sulforaphane (SUL), allyl isothiocyanate (AITC), indole-3-carbinol (I3C), and parthenolide (PTL), in the expression and degradation of Nrf2 and the induction of the antioxidant enzyme HO-1. SUL strongly induced Nrf2 protein expression and ARE-mediated transcription activation, retarded degradation of Nrf2 through inhibiting Keap1, and thereby activating the transcriptional expression of HO-1. AITC was also a potent inducer of Nrf2 protein expression, ARE-reporter gene and HO-1 but had little effect on delaying the degradation of Nrf2 protein. Although PTL and I3C could induce ARE reporter gene expression and Nrf2 to some extent, they were not as potent as SUL and AITC. However, PTL dramatically induced the HO-1 expression, which was comparable to SUL, while I3C had no effect. In addition, when treated with SUL and PTL, inhibition of proteasome by MG132 did not cause additional accumulation of Nrf2, suggesting the involvement of other degradation mechanism(s) in the presence of these compounds such as SUL and PTL. In summary, the results of our current study indicated that different chemopreventive compounds have different regulatory properties on the accumulation and degradation of Nrf2 as well as the induction of cellular antioxidant enzyme HO-1.

• Journal of Embryo Transfer
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• v.29 no.2
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• pp.101-109
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• 2014

Matrix Metalloproteinases (MMP)-2 and -9 are participated in embryo development, implantation, remodeling of epithelial cell and ovulation. The objective of this study is to evaluate an impact of MMP2 and MMP9 on embryonic developmental competence as well as gene expression profiles of in vitro-produced bovine embryos. After in vitro fertilization, embryos of all groups were transferred into IVC-2 medium treated with MMP2 and MMP9 to check the optimum concentration on the basis of embryo development competence and cell numbers. The optimum concentrations for MMP2 and 9 were 1,200 ng/ml and 300 ng/ml. The blastocyst development competence was not different among 1,200 ng/ml of MMP2 vs. 300 ng/ml of MMP9 vs. combined MMP2 + 9 vs. control groups ($41.46{\pm}10.66$ vs. $37.73{\pm}8.92$ vs. $45.11{\pm}11.41%$ vs. $41.59{\pm}11.88$, respectively). Furthermore, the developmental competences to hatching and hatched blastocysts were not also different among the same groups ($79.84{\pm}12.63$ vs. $83.3{\pm}17.46$ vs. $78.55{\pm}14.48%$ vs. $72.02{\pm}14.09$). In addition, total cell number was significantly (p<0.05) greater in blastocyst treated with MMP9 300 ng/ml among all treatment groups. On the other hand, there was no significant difference of ICM vs. TE ratio in all groups. The expression of five out of six genes (i.e., MMP2, MMP9, IFNt, SSLP1 and HNRNPA2B1) was different among the groups. The expression of IFNt and HNRNPA2B1 genes was significantly greater in MMP9 (p<0.05), but there was no difference of MMP9 expression between MMP2 and MMP9 group (p>0.05). The normalized expression of MMP2 and SSLP1 was greater in MMP2 than other groups (p<0.05). In conclusion, MMPs treatment during IVC-2 medium was remarkably effected on blastocyst developmental competence and gene expression profiles that are related to embryo quality and implantation.

• Journal of Fashion Business
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• v.13 no.6
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• pp.137-146
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• 2009

This study analyzed hierarchy of image for visual evaluation of flare skirt. This study analyzed expression words about flare skirt with frequency data of image expression words with different length and volume of flare. Stimuli for the study were set to be 4 different volume of flare ($90^{\circ}$, $180^{\circ}$, $270^{\circ}$, $360^{\circ}$) and 3 different length of skirt(48cm, 58cm, 68cm). Stimuli were made by using I-Designer which is Virtual Sewing System. From simulation of flare skirt, the subjects were asked to write down suggested adjective freely and selected 210 adjectives. With this, we chose total 38 adjectives considering frequencies in the pre-study. And we analyzed the combination process of expression words according to construction factor of flare skirt and hierarchy of image from dendrogram which was resulted by hierarchical cluster analysis. 'Feminine' got high score in all 12 flare skirt. When the skirt was short, it was vivid, and as the skirt got longer, ordinary and pure image showed. Also, as the volume of flare got larger, the average of visual effect was higher than visual image. Visual hierarchy construction according to construction factors of flare skirt could be divided into visual image and visual effect, and visual image was shown to be form 'A type - large volume of flare and short skirt length', 'H type-small volume of flare and short skirt length' and 'X type - large volume of flare and long skirt length'.

• Proceedings of the Korean Society of Plant Pathology Conference
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• 2003.10a
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• pp.81.1-81
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• 2003

Although plants have evolved to possess various defense mechanisms from local biotic and abiotic stressors, most of yield loss is caused by theses stressors. Recent studies have revealed that several different stress responsive reactions are inter-networking. Therefore, the identification and dissection of stress responsive genes is an essential and first step towards understanding of the global defense mechanism in response to various stressors. For this purpose, we applied cDNA microarray analysis, because it has powerful ability to monitor the global gene expression in a specific situation. To date, more than 10,000 non-redundant genes were identified from seven different cDNA libraries and deposited in our EST database (http://plant.pdrs.re.kr/ks200201/pepper.html). For this study, we have built 5K cDNA microarray containing 4,685 unigene clones from three different cDNA libraries. Monitoring of gene expression profiles of hot pepper interactions with biotic stress, abiotic stresses and chemical treatments will be presented. Although this work shows expression profiling at the sub-genomic level, this could be a good starting point to understand the complexity of global defense mechanism in hot pepper.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2000.11a
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• pp.59-60
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• 2000

The past few years have seen a dramatic increase in gene expression data on the basis of DNA microarrays or DNA chips. Going beyond a generic view on the genome, microarray data are able to distinguish between gene populations in different tissues of the same organism and in different states of cells belonging to the same tissue. This affords a cell-wide view of the metabolic and regulatory processes under different conditions, building an effective basis for new diagnoses and therapies of diseases. In this talk we present machine learning techniques for effective mining of DNA microarray data. A brief introduction to the research field of machine learning from the computer science and artificial intelligence point of view is followed by a review of recently-developed learning algorithms applied to the analysis of DNA chip gene expression data. Emphasis is put on graphical models, such as Bayesian networks, latent variable models, and generative topographic mapping. Finally, we report on our own results of applying these learning methods to two important problems: the identification of cell cycle-regulated genes and the discovery of cancer classes by gene expression monitoring. The data sets are provided by the competition CAMDA-2000, the Critical Assessment of Techniques for Microarray Data Mining.

• Journal of Microbiology and Biotechnology
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• v.19 no.8
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• pp.774-780
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• 2009

Flammulina velutipes is a popular edible basidiomycete mushroom found in East Asia and is commonly known as winter mushroom. Mushroom development showing dramatic morphological changes by different environmental factors is scientifically and commercially interesting. To create a genetic database and isolate genes regulated during mushroom development, cDNA libraries were constructed from three developmental stages of mycelium, primordium, and fruit body in F. velutipes. We generated a total of 5,431 expressed sequence tags (ESTs) from randomly selected clones from the three cDNA libraries. Of these, 3,332 different unique genes (unigenes) were consistent with 2,442 (73%) singlets and 890 (27%) contigs. This corresponds to a redundancy of 39%. Using a homology search in the gene ontology database, the EST unigenes were classified into the three categories of molecular function (28%), biological process (29%), and cellular component (6%). Comparative analysis found great variations in the unigene expression pattern among the three different unigene sets generated from the cDNA libraries of mycelium, primordium, and fruit body. The 19-34% of total unigenes were unique to each unigene set and only 3% were shared among all three unigene sets. The unique and common representation in F. velutipes unigenes from the three different cDNA libraries suggests great differential gene expression profiles during the different developmental stages of F. velutipes mushroom.

• Journal of Microbiology and Biotechnology
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• v.27 no.1
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• pp.112-121
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• 2017

Edwardsiella tarda is a gram-negative pathogenic bacterium in aquaculture that can cause hemorrhagic septicemia in fish. Many secreted proteins have already been identified as virulent factors of E. tarda. Moreover, since virulent phenotypes are based on the expression regulation of virulent genes, understanding the expression profile of virulent genes is important. A quantitative RT-PCR is one of the preferred methods for determining different gene expressions. However, this requires the selection of a stable reference gene in E. tarda, which has not yet been systematically studied. Accordingly, this study evaluated nine candidate reference genes (recA, uup, rpoB, rho, topA, gyrA, groEL, rpoD, and 16S rRNA) using the Excel-based programs BestKeeper, GeNorm, and NormFinder under different culture conditions. The results showed that 16S rRNA was more stable than the other genes at different culture growth phases. However, at the same culture time, topA was identified as the reference gene under the conditions of different strains, different culture media, and infection, whereas gyrA was identified under the condition of different temperatures. Thus, in experiments, the expression of gapA and fbaA in E. tarda was analyzed by RT-qPCR using 16S rRNA, recA, and uup as the reference genes. The results showed that 16S rRNA was the most suitable reference gene in this analysis, and that using unsuitable reference genes resulted in inaccurate results.

• Asian-Australasian Journal of Animal Sciences
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• v.19 no.2
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• pp.165-170
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• 2006

Using the somatic cell hybrid panel (SCHP) and radiation hybrid (IMpRH) panel, porcine SOCS2 gene was mapped at SSC5 (1/2) q21-q24 and closely linked with SW1383 marker (47 cR in distance), while SOCS3 gene was assigned to SSC12p11-(2/3p13) and closely linked with SW2490 (43 cR). The reverse transcriptase-polymerase chain reaction (RT-PCR) was performed to detect the expression of these two genes in the different tissues and the results showed that both SOCS2 and SOCS3 genes were widely expressed in tissues investigated (heart, liver, spleen, lung, kidney skeletal muscle, fat and brain), although some tissues showed lower gene expression. Moreover, SOCS2 and SOCS3 genes had different expression levels at different stages, in different tissues and in different breeds. A G/A substitution, which can be recognized by restriction enzyme of Cfr421, was observed in 5' untranslated region (5'-UTR) of SOCS2 gene. The allele frequencies was investigated by PCR-restriction fragment length polymorphism (PCR-RFLP) method and it showed that the allele frequency among Dahuabai, Erhualian, Yushan, Qingping, Large white and Landrace tested were different. Association analysis in a cross experimental populations revealed no significant association between the SOCS2 gene polymorphism and the economic traits investigated. The full-length coding regions (CDs) of porcine SOCS3 gene was obtained by RT-PCR.

• Journal of Microbiology and Biotechnology
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• v.17 no.8
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• pp.1390-1393
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• 2007

In this study, three of the representative EDCs, $17{\beta}$-estradiol, bisphenol A, and styrene, were employed to find their mode of toxic actions in E. coli. To accomplish this, four different stress response genes, recA, katG, fabA, and grpE genes, were used as a representative for DNA, oxidative, membrane, or protein damage, respectively. The expression levels of these four genes were quantified using a real-time RT-PCR after challenge with three different EDCs individually. Bisphenol A and styrene caused high-level expression of recA and katG genes, respectively, whereas $17{\beta}$-estradiol made no significant changes in expression of any of those genes. These results lead to the classification of the mode of toxic actions of EDCs on E. coli.