• Journal of Applied Biological Chemistry
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• v.64 no.1
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• pp.39-48
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• 2021

Droughts are one of the abiotic stresses that hinders the growth and productivity of crop plants. Coping with abiotic stress is necessary to understand the molecular regulatory networks that makes plants respond to adverse environmental conditions. In our experiment to find a combination that can cope with abiotic stress (respond to drought), we screened 5 stress-inducible promoters that are expressed only under stress conditions. This founded 36 cis-elements in stress-inducible promoters. With the result we designed 2 synthetic promoters (BL1, BL2) for fine-controlled regulation by assembling cis-elements from the native promoters, which are expressed only under stress caused by droughts. Analysis of the transgenic plant (BL1-GUS, BL2-GUS) showed that the synthetic promoters increased the expression of β-glucuronidase (GUS) in transgenic plants under desiccation. Also in the transient activation assay demonstrated that synthetic promoters induced the co-transformation of effector DREB1A and DREB2C. These results expect that the synthetic promoter with a combination of drought-specific elements can be used to respond to various abiotic stress and is resistant to stress without causing growth retardation.

• The Korean Journal of Ecology
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• v.12 no.1
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• pp.37-49
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• 1989

When the light stimulus was presented continuously, habituations were formed, after 13 and 14 hrs in amoeba and planaria, repectively. As amoeba more habituated, the light-escaping velocity of streaming was decreased with a negative-exponential function. in two-dimensional electrophoretic patterns of proteins of amoeba habituated, a newly synthesized protein (pI 7.0, MW 20 kD) was detected. Therefore, it is conjectured that similarity or commonality may exist between amoeba and planaria habituations to light, and in these behavioral modifications, specific protein(s) may be involved in molecular level.

• Bulletin of the Korean Chemical Society
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• v.29 no.1
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• pp.89-93
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• 2008

The key step in a strategy for the synthesis of (+)-lactacystin involving photocyclization reaction of a cyclopenta-fused pyridinium salt has been probed by using a model substrate. Observations made in this effort led to the discovery of a highly unusual cascade process that leads to stereoselective formation of an interesting tricyclic carbamate. The results of this study are presented and discussed in the context of a (+)-lactacystin synthetic approach.

• Genomics & Informatics
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• v.11 no.1
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• pp.55-57
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• 2013

Growing numbers of studies employ cell line-based systematic short interfering RNA (siRNA) screens to study gene functions and to identify drug targets. As multiple sources of variations that are unique to siRNA screens exist, there is a growing demand for a computational tool that generates normalized values and standardized scores. However, only a few tools have been available so far with limited usability. Here, we present siMacro, a fast and easy-to-use Microsoft Office Excel-based tool with a graphic user interface, designed to process single-condition or two-condition synthetic screen datasets. siMacro normalizes position and batch effects, censors outlier samples, and calculates Z-scores and robust Z-scores, with a spreadsheet output of >120,000 samples in under 1 minute.

• BMB Reports
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• v.44 no.10
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• pp.669-673
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• 2011

Human methionine sulfoxide reductase B3A (hMsrB3A) is an endoplasmic reticulum (ER) reductase that catalyzes the stereospecific reduction of methionine-R-sulfoxide to methionine in proteins. In this work, we identified an antimicrobial peptide from hMsrB3A protein. The N-terminal ER-targeting signal peptide (amino acids 1-31) conferred an antimicrobial effect in Escherichia coli cells. Sequence and structural analyses showed that the overall positively charged ER signal peptide had an Argand Pro-rich region and a potential hydrophobic ${\alpha}$-helical segment that contains 4 cysteine residues. The potential ${\alpha}$-helical region was essential for the antimicrobial activity within E. coli cells. A synthetic peptide, comprised of 2-26 amino acids of the signal peptide, was effective at killing Gram-negative E. coli, Klebsiella pneumoniae, and Salmonella paratyphi, but had no bactericidal activity against Gram-positive Staphylococcus aureus.

• BMB Reports
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• v.31 no.5
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• pp.419-426
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• 1998

The nuclear hormone receptor superfamily currently includes approximately equal numbers of conventional receptors and orphan receptors, which do not have known ligands. Here, we review recent progress from this laboratory on three orphans, two of which are moving from orphan to conventional receptor status. Perhaps the most unusual is CAR, which is a constitutive transactivator in the absence of ligands but becomes transcriptionally inactive in the presence of its ligands, which are androgen metabolites. The response of CAR to its ligands is thus opposite to that of the conventional receptor paradigm. RIP14 (also known as FXR) is activated by both all-trans retinoic acid and a synthetic retinoid previously thought to specifically target the retinoic acid receptors (RARs), and thus appears to be a novel retinoid receptor. Finally, SHP is a novel orphan that lacks a DNA binding domain and interacts with a number of other receptor superfamily members. While it generally inhibits its targets, including CAR, the retinoid X receptor (RXR), and the estrogen receptor (ER), it stimulates transactivation by the orphan SF-1.

• Molecules and Cells
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• v.27 no.6
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• pp.689-695
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• 2009

Chemically synthesized small interfering RNAs (siRNAs) can specifically knock-down expression of target genes via RNA interference (RNAi) pathway. To date, the length of synthetic siRNA duplex has been strictly maintained less than 30 bp, because an early study suggested that double-stranded RNAs (dsRNAs) longer than 30 bp could not trigger specific gene silencing due to the induction of non-specific antiviral interferon responses. Contrary to the current belief, here we show that synthetic dsRNA as long as 38 bp can result in specific target gene silencing without non-specific antiviral responses. Using this longer duplex structure, we have generated dsRNAs, which can simultaneously knock-down expression of two target genes (termed as dual-target siRNAs or dsiRNAs). Our results thus demonstrate the structural flexibility of gene silencing siRNAs, and provide a starting point to construct multifunctional RNA structures. The dsiRNAs could be utilized to develop a novel therapeutic gene silencing strategy against diseases with multiple gene alternations such as viral infection and cancer.

• BMB Reports
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• v.28 no.1
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• pp.83-86
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• 1995

In the course of screening for new aminopeptidase M inhibitors which were expected to be analgesic, immunopotentiating, or anti-metastatic agents, the novel synthetic substance MR-387C[(2S,3R)-3-amino-2-hydroxy-4-phenylbutanoyl-L-valyl-L-prolyl-L-leucine] (M.W. 504 daltons) was obtained. It was competitive with the substrate and had an $IC_{50}$ value of $0.04\;{\mu}m/ml$ ($7.9{\times}10^{-8}\;M$) and an inhibition constant ($K_i$) of $3.8{\times}10^{-8}\;M$. This novel MR-387C was compared with various known inhibitors of aminopeptidase M. It inhibited the enzyme more strongly than any other microorganism-originated inhibitor, except probestin.

• Bulletin of the Korean Chemical Society
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• v.34 no.7
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• pp.1972-1984
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• 2013

Microtubules play an important role in intracellular transport, mobility, and particularly mitosis. Paclitaxel (Taxol$^{TM}$) and paclitaxel-like compounds have been shown to be anti-tumor agents useful for various human tumors. Paclitaxel-like compounds operate by stabilizing microtubules through interface binding at the interface between two ${\beta}$-tubulin monomers in adjacent protofilaments. In this paper we present the elucidation of the structural features of paclitaxel and paclitaxel-like compounds (e.g., epothilones) with microtubule stabilizing activities, and relate their activities to spatial and chemical features of the molecules. CATALYST program was used to generate three-dimensional quantitative structure activity relationships (3D-QSARs) resulting in 3D pharmacophore models of epothilone- and paclitaxel-derivatives. Pharmacophore models were generated from diverse conformers of these compounds resulting in a high correlation between experimental and predicted biological activities (r = 0.83 and 0.91 for epothilone and paclitaxel derivatives, respectively). On the basis of biological activities of the training sets, five- and four-feature pharmacophore hypotheses were generated in the epothilone and paclitaxel series. The validation of generated hypotheses was achieved by using twelve epothilones and ten paclitaxels, respectively, which are not in the training sets. The clustering (grouping) and merging techniques were used in order to supplement spatial restrictions of each of hypothesis and to develop more comprehensive models. This approach may be of use in developing novel inhibitor candidates as well as contributing a better understanding of structural characters of many compounds useful as anticancer agents targeting microtubules.

• Preventive Nutrition and Food Science
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• v.7 no.4
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• pp.454-460
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• 2002

While atherosclerosis is a major killer, there is now concern that mortality from the disease will increase due to the rising incidence of type II diabetes. Because diet can potentially influence both diseases, it is important to elucidate the role of diet in the progression of atherosclerosis. In addition, the mechanisms involved in dietary-related alterations of the disease need to be defined to guide public health recommendations to reduce athero-sclerosis incidence and limiting unwanted side effects. Since diet is thought to play a role in atherosclerosis even without added complications due to type II diabetes, reducing the incidence of that metabolic disease will not be enough. While evidence is increasing that high intake of carbohydrate can lead to type II diabetes and atherosclerosis, the preponderance of existing evidence indicates that intake of specific fats as a major dietary causal factor. It has recently been hypothesized that a dietary fat link to atherosclerosis may depend partly on the activity of a transcriptional regulator, the peroxisome proliferator activated receptors (PPAR). Thusfar, PPAR $\alpha$, $\beta$/$\delta$ and ${\gamma}$, have been shown to play a major role in metabolism, inflammation, and cancer. Furthermore, PPAR may regulate specific processes associated with atherosclerosis such as triglyceride and low density lipoprotein (LDL) metabolism; the reverse cholesterol transport pathway; lipid accumulation within plaques; the local inflammatory response and plaque stability. Synthetic ligands for PPAR have been developed; however, natural ligands include specific fatty acids and their metabolites. Though the role of PPAR in atherosclerosis has been reported with respect to synthetic ligands, additional studies need to be done with established and possible natural ligands. In this review, we will focus on the relation of dietary fat to PPAR alteration of atherosclerosis.