• Korean Journal of Agricultural Science
• /
• v.37 no.3
• /
• pp.367-371
• /
• 2010

Farnesyl diphosphate synthase (FPS) catalyzes the biosynthesis of farnesyl diphosphate, a precursor for many important terpenoid products. A cDNA encoding FPS was first isolated from Allium sativum (AsFPS) using rapid amplification of cDNA ends (RACE) PCR. The sequence of AsFPS contains an open reading frame encoding a protein of 341 amino acids with a predicted molecular mass of 39.61 kDa. Alignment of AsFPS deduced amino acid revealed high identities with other plants ranging from 79% to 85% and showed 2-high conserved aspartate-rich motifs known to be important for FPS activity. Furthermore, AsFPS expression was stronger in the green organs such as bulbils, scapes, leaves, stems, but weaker in bulbs and roots than on-green organs of A. sativum.

• Journal of Integrative Natural Science
• /
• v.8 no.2
• /
• pp.89-98
• /
• 2015

Chemoattractant receptor homologous molecule expressed on Th2 cells (CRTh2) is a G-protein coupled receptor targeted for inflammatory diseases such as asthma, allergic rhinitis and atopic dermatitis. In this study, pharmacophore modeling and comparative molecular field analysis (CoMFA) were performed on the series of 2-(2-(benzylthio)-1H-benzo[d]imidazol-1-yl) acetic acids derivatives. Five highly active compounds were used for generation of pharmacophore models using GASP module. The best pharmacophore model was selected and used as template for the alignment of compounds which was used for CoMFA analysis. The best predictions obtained for CoMFA was $q^2=0.545$, $r^2=0.756$. The predictive ability of the model was investigated using 15 test set compounds. Contour maps suggested that presence of bulky substituents at $5^{th}$ position of benzene ring connected to suphur atoms attached to imidazol ring will increase the activity of the compounds. The results obtained from this study will be useful to design more potent CRTh2 antagonists.

• The Plant Pathology Journal
• /
• v.30 no.1
• /
• pp.96-101
• /
• 2014

The molecular features of Pseudomonas syringae pv. actinidiae strains isolated in Korea were compared with strains isolated in Japan and Italy. Sequencing of eight P. syringae pv. actinidiae and three P. syringae pv. theae strains revealed a total of 44 single nucleotide polymorphisms across 4,818 bp of the concatenated alignment of nine genes. A multiplex PCR assay was developed for the detection of P. syringae pv. actinidiae and for the specific detection of recent haplotype strains other than strains isolated since the 1980s in Korea. The primer pair, designated as TacF and TacR, specifically amplified a 545-bp fragment with the genomic DNA of new haplotype of P. syringae pv. actinidiae strains. A multiplex PCR conducted with the TacF/TacR primer pair and the universal primer pair for all P. syringae pv. actinidiae strains can be simultaneously applied for the detection of P. syringae pv. actinidiae and for the differentiation of new haplotype strains.

• Genomics & Informatics
• /
• v.6 no.2
• /
• pp.72-76
• /
• 2008

Hypoxia-inducible factor $1{\alpha}\;(HIF1{\alpha})$ is a transcription factor that plays a key role in the adaptation of cells to low oxygen stress and oxygen homeostasis. The oxygen-dependent degradation (ODD) domain of $HIF1{\alpha}$ is responsible for the negative regulation of $HIF1{\alpha}$ in normoxia. The interactions of the $HIF1{\alpha}$ ODD domain with partner proteins such as von Hippel-Lindau tumor suppressor (pVHL) and p53 are mediated by two sequence motifs, the N- and C-terminal ODD(NODD and CODD). Multiple sequence alignment with $HIF1{\alpha}$ homologs from human, monkey, pig, rat, mouse, chicken, frog, and zebrafish has demonstrated that the NODD and CODD motifs have noticeably high conservation of the primary sequence across different species and isoforms. In this study, we carried out molecular dynamics simulation of the structure of the $HIF1{\alpha}$ CODD motif in complex with the p53 DNA-binding domain (DBD). The structure reveals specific functional roles of highly conserved residues in the CODD sequence motif of $HIF1{\alpha}$ for the recognition of p53.

• BMB Reports
• /
• v.38 no.4
• /
• pp.440-446
• /
• 2005

A cDNA that was rapidly induced upon abscisic acid, cold, drought, mechanical wounding and to a lesser extent, by high salinity treatment, was isolated from Arabidopsis seedlings. It was classified as DREB subfamily member based on multiple sequence alignment and phylogenetic characterization. Since it encoded a protein with a typical ERF/AP2 DNA-binding domain and was closely related to the TINY gene, we named it TINY2. Gel retardation assay revealed that TINY2 was able to form a specific complex with the previously characterized DRE element while showed only residual affinity to the GCC box. When fused to the GAL4 DNA-binding domain, either full-length or its C-terminus functioned effectively as a trans-activator in the yeast one-hybrid assay while its N-terminus was completely inactive. Our data indicate that TINY2 could be a new member of the AP2/EREBP transcription factor family involved in activation of down-stream genes in response to environmental stress.

• BMB Reports
• /
• v.42 no.5
• /
• pp.271-276
• /
• 2009

Sweetpotato (Ipomoea batatas (L). Lam.) is relatively tolerant to unfavorable growth conditions such as drought, yet has not been exploited to provide a better understanding of the molecular basis of drought stress tolerance. We obtained 983 high-quality expressed sequence tags of 100 bp or longer (average length of 700 bp) from cDNA libraries of detached white fibrous root tissues by subjecting them to dehydration for 6 h. The 431 cDNAs were each assigned a function by alignment using the BLASTX algorithm. Among them, three genes associated with various abiotic stresses and nine genes not previously associated with drought stress were selected for expression pattern analysis through detailed reverse transcription-polymerase chain reaction. The direct and indirect relationships of the 12 genes with drought tolerance mechanisms were ascertained at different developmental stages and under various stress conditions.

• BMB Reports
• /
• v.39 no.6
• /
• pp.782-787
• /
• 2006

A new protein was cloned and identified as the sixth subunit of Choristoneura fumiferana origin recognition complex (CfORC6). The newly identified 43 kDa protein CfORC6 is much bigger than DmORC6 (25.7 kDa) and HsORC6 (28.1 kDa), though it's 23.85% identical to DmORC6 and 23.81% identical to HsORC6. Although the molecular weight of CfORC6 is close to ScORc6 (50 kDa), CfORC6 is only 14.03% identical to ScORC6. By alignment, it was found that the N-terminal of CfORC6 has about 30% identities with other ORC6s, but about 100aa of C-terminal of CfORC6 has no identity with other ORC6s. Like ScORC6, CfORC6 has many potential phosphorylation sites, (S/T)PXK. Like DmORC6, CfORC6 has leucine-rich region in the relevant site. Northern Blot showed that CfORC6 mRNA is about 2,000nt. Southern Blot confirmed that there is one copy of CfORC6 gene in spruce budworm genome. Western blot showed that infection of Cf124T cells with CfMNPV didn't affect the expression levels of CfORC6, at least up to 26 hr post infection.

• Fisheries and Aquatic Sciences
• /
• v.13 no.4
• /
• pp.263-271
• /
• 2010

G protein-coupled receptors (GPCR) constitute the largest superfamily of cell membrane receptors, mediating diverse signal-transduction pathways. The melanocortin 4 receptor (MC4R) has been of interest for its physiological role and size, one of the smallest among the GPCRs, which makes it a good model system for the structural study of GPCRs. To study the molecular structure and tissue-specific expression of MC4R in olive flounder (Paralichthys olivaceus), the full-length MC4R gene was obtained using PCR amplification of genomic DNA as well as cDNA synthesis. Sequence analysis of the gene indicates that 978 bp of the MC4R gene encodes 325 amino acids without introns. Sequence alignment with the MC4Rs from other fish shows the highest degree of identity (96%) between Paralichthys olivaceous and Verasper moseri, followed by Takifugu rubripes and Tetraodon nigroviridis (89%). RNA was isolated from various tissues to examine the tissue distribution of MC4R by using RT-PCR. The results showed major expression of MC4R in the liver, brain, and eye, which is consistent with the expression pattern in other fish belonging to the order Pleuronectiformes.

• Proceedings of the Korean Vacuum Society Conference
• /
• 2010.08a
• /
• pp.291-291
• /
• 2010

Electron-beam lithography (EBL) process is a versatile tool for a fabrication of nanostructures, nano-gap electrodes or molecular arrays and its application to nano-device. However, it is not appropriate for the fabrication of sub-5 nm features and high-aspect-ratio nanostructures due to the limitation of EBL resolution. In this study, the precision assembly and alignment of DNA molecule was demonstrated using sub-5 nm nanostructures formed by a combination of conventional electron-beam lithography (EBL) and plasma ashing processes. The ma-N2401 (EBL-negative tone resist) nanostructures were patterned by EBL process at a dose of $200\;{\mu}C/cm2$ with 25 kV and then were ashed by a chemical dry etcher at microwave (${\mu}W$) power of 50 W. We confirmed that this method was useful for sub-5 nm patterning of high-aspect-ratio nanostructures. In addition, we also utilized the surface-patterning technique to create the molecular pattern comprised 3-(aminopropyl) triethoxysilane (APS) as adhesion layer and octadecyltrichlorosilane (OTS) as passivation layer. DNA-templated gold nanoparticle chain was attached only on the sub-5 nm APS region defined by the amine groups, but not on surface of the OTS region. We were able to obtain DNA molecules aligned selectively on a SiO2/Si substrate using atomic force microscopy (AFM).

• International Journal of Industrial Entomology and Biomaterials
• /
• v.5 no.1
• /
• pp.93-102
• /
• 2002

We have cloned and characterized the complete fibroin light chain gene from the silkworm Baekok-Jam, Bombyx mori, a recommended variety in Korea. It consists of seven exons and six introns. It consists of 14,663 nucleotides long with an open reading frame of 786 nucleotides that encodes a protein of 262 amino acid residues with a molecular mass of approximately 26,000 dalton. The amino acid alignment revealed that the Baekok-Jam fibroin light chain had 98.5 % protein sequence identity to J139 strain: differed at four amino acid positions (11, 46, 80 and 123). The Northern hybridization analysis showed that the Baekok-Jam fibroin light chain gene was specifically expressed in the posterior silk gland.