• Journal of Korean Society of Forest Science
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• v.102 no.2
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• pp.223-228
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• 2013

Phytoplasmas were detected consistently in 42 mulberry cultivars showing dwarf disease using DNA analysis by amplification with phytoplasma universal primer pairs P1/P7 (about 1.8 kb and R16F2n/R2 (about 1.2 kb). The point mutation from 42 cultivars of mulberry tree was detected by single-strand conformation polymorphism (SSCP) analysis. The SSCP profiles were clearly observed from all of cultivars in 8% polyacrylamide gel, electrophoresizing for and running 8-15 hrs. at 150V, $10^{\circ}C$. The MD and JWB phytoplasma PCR products was mixed and electrophoresis was performed to detect their polymorphism. In this results, the SSCP profiles of all bands of MD and JWB were analyzed on single lane and were distinct in their each of band patterns. The SSCP analysis was possible to detect of 1.8 kb and 1.2 kb nucleotide size and near close band patterns were distinct by mix of two samples. Previously, it was only possible to detect of point mutation under 600 bp nucleotide sequence by SSCP analysis but this modification of SSCP technique was possible to detect clearly SSCP band patterns of about 1.8 kb and 1.2 kb nucleotides.

• Molecules and Cells
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• v.26 no.2
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• pp.206-211
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• 2008

HI0381 of Haemophilus influenzae was investigated by circular dichroism (CD) and nuclear magnetic resonance (NMR) spectroscopy. HI0381 is a 153-residue peptidoglycan-associated outer membrane lipoprotein, and a part of the larger Tol/Pal network. Here, we report its backbone $^1H$, $^{15}N$, and $^{13}C$ resonance assignments, and secondary structure predictions. About 97% of all of the $^1HN$, $^{15}N$, $^{13}CO$, $^{13}C{\alpha}$, and $^{13}C{\beta}$ resonances covering 131 non-proline residues of the 134 residue, mature protein, were clarified by sequential and specific assignments. CSI and TALOS analyses revealed that HI0381 contains five ${\alpha}$-helices and five ${\beta}$-strands. To characterize the structure of HI0381, the effects of pH and salt concentration were investigated by CD. In addition, the structural changes occurring when HI0381 was in a membranous environment were investigated by comparing its HSQC spectra and CD data in buffer and in DPC micelles; the results showed that helix ${\alpha}4$ and strand ${\beta}4$ became aligned with the membrane. We conclude that the conformation of HI0381 is affected by the membrane environment, implying that its folded state is directly related to its function.

• Journal of the Korean Wood Science and Technology
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• v.38 no.1
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• pp.1-10
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• 2010

In this study, to study an effective use and improve strength performances of woods and wood-based materials, three-ply hybrid laminated woods which are composed of spruce in the face and three kinds of wood-based boards (MDF, PB, OSB) in the core were manufactured, and the effect of constitution elements used for the core laminae on bending creep performances was investigated. The shape of creep curves showed exponential function plots which the upper right side was increased, and differed among the kinds of wood-based boards used for the core laminae of hybrid laminated wood. The creep deformation perpendicular to the grain of faces of hybrid laminated woods was in order $C_{\perp}$(P) > $C_{\perp}$(M) > $C_{\perp}$(O) with PB, MDF and OSB in the core, respectively. It was found that the creep deformation arranged with OSB in the core had 2 times smaller than those arranged with MDF and PB in the core. By hybrid laminating, the creep deformation of spruce perpendicular to the grain was markedly decreased. On the other hand, the creep deformation parallel to the grain of the faces ($C_{\parallel}$ type) of hybrid laminated woods was in order $C_{\parallel}$(P) > $C_{\parallel}$(O) > $C_{\parallel}$(M) with PB, OSB and MDF in the core. The ratios among three hybrid laminated woods were considerably decreased, especially the difference between $C_{\parallel}$(P) and $C_{\parallel}$(O) hybrid laminated woods arranged with PB and OSB in the core was very small. These values showed 0.108~0.464 times smaller than creep deformation of three wood-based boards and it was found that creep deformation of three wood-based boards was considerably decreased by hybrid laminating. Creep anisotropy of hybrid laminated woods was greater in creep deformation than in initial deformation, whereas it was found that the values was much smaller than that of spruce parallel laminated woods.

• Asian-Australasian Journal of Animal Sciences
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• v.29 no.9
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• pp.1256-1264
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• 2016

Adrenergic, alpha-1B-, receptor (ADRA1B) and peroxisome proliferator-activated receptor gamma, coactivator 1 beta (PPARGC1B) genes are involved in regulation of hen ovarian development. In this study, these two genes were investigated as possible molecular markers associated with hen-housed egg production, egg weight (EW) and body weight in Chinese Dagu hens. Samples were analyzed using the polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) technique, followed by sequencing analysis. Two novel single nucleotide polymorphisms (SNPs) were identified within the candidate genes. Among them, an A/G transition at base position 1915 in exon 2 of ADRA1B gene and a T/C mutation at base position 6146 in the 3'- untranslated region (UTR) of PPARGC1B gene were found to be polymorphic and named SNP A1915G and T6146C, respectively. The SNP A1915G (ADRA1B) leads to a non-synonymous substitution (aspartic acid 489-to-glycine). The 360 birds from the Dagu population were divided into genotypes AA and AG, allele A was found to be present at a higher frequency. Furthermore, the AG genotype correlated with significantly higher hen-housed egg production (HHEP) at 30, 43, 57, and 66 wks of age and with a higher EW at 30 and 43 wks (p<0.05). For the SNP T6146C (PPARGC1B), the hens were typed into TT and TC genotypes, with the T allele shown to be dominant. The TC genotype was also markedly correlated with higher HHEP at 57 and 66 wks of age and EW at 30 and 43 wks (p<0.05). Moreover, four haplotypes were reconstructed based on these two SNPs, with the AGTC haplotype found to be associated with the highest HHEP at 30 to 66 wks of age and with higher EW at 30 and 43 wks (p<0.05). Collectively, the two SNPs identified in this study might be used as potential genetic molecular markers favorable in the improvement of egg productivity in chicken breeding.

• Asian-Australasian Journal of Animal Sciences
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• v.23 no.7
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• pp.863-866
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• 2010

Myostatin, which is also known as growth and differentiation factor 8 (GDF8), has been reported to act as a negative regulator of skeletal muscle development. Variation in the myostatin gene (MSTN) has been associated with variation in muscularity in certain "meaty" sheep breeds. Polymerase Chain Reaction-Single Strand Conformational Polymorphism (PCR-SSCP) analysis was used to investigate allelic variation in the previously described g+6223G>A single-nucleotide polymorphism (SNP) in the 3' untranslated region (3' UTR) of MSTN. The sheep studied were 79 New Zealand (NZ) Romney lambs derived from a single sire heterozyous for g+6223G>A, which is in itself notable as this polymorphism has not been described previously in this breed. Allelic variation was observed to be associated with an abnormal gender ratio (p = 0.046) in the progeny. The presence of allele A was observed to have an effect (p<0.05) on birth weight, mean loin yield, proportion yield loin and total muscle yield. Allelic variation did not significantly affect mean shoulder yield, leg yield, proportion yield shoulder and proportion yield leg. This preliminary result suggests that while the A allele at MSTN g+6223 appears to improve some valuable traits in NZ Romney sheep, further research is required to understand if and how it may affect other traits.

• Asian-Australasian Journal of Animal Sciences
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• v.28 no.6
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• pp.782-787
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• 2015

The myogenic regulatory factors is a family of transcription factors that play a key role in the development of skeletal muscle fibers, which are the main factors to affect the meat taste and texture. In the present study, we performed candidate gene analysis to identify single-nucleotide polymorphisms in the MyoD, Myf5, MyoG, and Mrf4 genes using polymerase chain reaction-single strand conformation polymorphism in 360 Erlang Mountain Chickens from three different housing systems (cage, pen, and free-range). The general linear model procedure was used to estimate the statistical significance of association between combined genotypes and muscle fiber traits of chickens. Two polymorphisms (g.39928301T>G and g.11579368C>T) were detected in the Mrf4 and MyoD gene, respectively. The diameters of thigh and pectoralis muscle fibers were higher in birds with the combined genotypes of GG-TT and TTCT (p<0.05). Moreover, the interaction between housing system and combined genotypes has no significant effect on the traits of muscle fiber (p>0.05). Our findings suggest that the combined genotypes of TT-CT and GG-TT might be advantageous for muscle fiber traits, and could be the potential genetic markers for breeding program in Erlang Mountain Chickens.

• Bulletin of the Korean Chemical Society
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• v.27 no.4
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• pp.568-572
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• 2006

To study the effect of sequence on DNA structure, the two decamer crystal structures one alternating,d(GTACGCGTAC), and the other non-alternating, d(GGCCGCGGCC), were solved. Crystals of both decamers belong to the hexagonal space group $P6_122$, with one strand in the asymmetric unit. The unit cell constants of the alternating decamer are a = b = 39.26 $\AA$, c = 77.70 $\AA$. The structure was refined with 1,828 reflections from 8.0 to 2.0 Aresolution to an R value of 21.3% with all DNA atoms and 63 water molecules. The isomorphous non-alternating decamer had unit cell dimensions of a = b = 39.05 $\AA$, c = 82.15 $\AA$. The structure was refined with 2,423 reflections from 8.0 to 2.0 $\AA$ resolution to a final R value of 22.2% for all DNA atoms and 65 water molecules. Although the average helical parameters of the decamers are typical of A-DNAs, there are some minor differences between them. The helical twist, rise, x-displacement, inclination and roll alternate in the alternating decamer, but do not in the non-alternating decamer. The backbone conformations in both structures show some differences; the residue G(7) of the alternating decamer is trans for $\alpha$ and $\gamma$ while the trans conformations are observed at the residue G(8) of the non-alternating decamer.

• Molecules and Cells
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• v.39 no.6
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• pp.495-500
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• 2016

We have solved the crystal structure of a predicted fructose-specific enzyme $IIB^{fruc}$ from Escherichia coli ($EcEIIB^{fruc}$) involved in the phosphoenolpyruvate-carbohydrate phosphotransferase system transferring carbohydrates across the cytoplasmic membrane. $EcEIIB^{fruc}$ belongs to a sequence family with more than 5,000 sequence homologues with 25-99% amino-acid sequence identity. It reveals a conventional Rossmann-like ${\alpha}-{\beta}-{\alpha}$ sandwich fold with a unique ${\beta}$-sheet topology. Its C-terminus is longer than its closest relatives and forms an additional ${\beta}$-strand whereas the shorter C-terminus is random coil in the relatives. Interestingly, its core structure is similar to that of enzyme $IIB^{cellobiose}$ from E. coli ($EcIIB^{cel}$) transferring a phosphate moiety. In the active site of the closest $EcEIIB^{fruc}$ homologues, a unique motif CXXGXAHT comprising a P-loop like architecture including a histidine residue is found. The conserved cysteine on this loop may be deprotonated to act as a nucleophile similar to that of $EcIIB^{cel}$. The conserved histidine residue is presumed to bind the negatively charged phosphate. Therefore, we propose that the catalytic mechanism of $EcEIIB^{fruc}$ is similar to that of $EcIIB^{cel}$ transferring phosphoryl moiety to a specific carbohydrate.

• Journal of Life Science
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• v.19 no.9
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• pp.1218-1225
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• 2009

Difractose anhydrides (DFAs) is studied as a sweetener for diabetics because of its structural property. DFAs have four types: DFA I, III, IV (degradation of levan) and V (degradation of inulin). Especially, DFA IV has been shown to enhance the absorption of calcium in experiments using rats. Levan fructotransferase is an enzyme for producing di-d-fructose-2,6':6,2-dianhydride (DFA IV). To identify structural characterization, we purified wild-type and mutants (D63A, D195N and N85S) of levan fructotransferase (LFTase) from Microbacterium sp. AL-210. These proteins were purified to apparent homogeneity by Ni-NTA affinity column, Q-sepharose ion exchange and gel filtration chromatography and detected by SDS-PAGE. They were also analyzed by circular dichroism (CD) measurements, JNET secondary structure prediction, activity measurements at various temperatures, and pH analysis. The optimum pH for the enzyme-catalyzed reaction was pH 7.5 and optimum temperature was observed at $55^{\circ}C$. Along with wild-type LFTase, mutants were analyzed by CD measurement, fluorescence analysis and differential scanning calorimetry (DSC). N85S showed less $\alpha$-helix and more $\beta$ strand than others. Also, N85S showed almost the same curve as wild-type in their steady-state fluorescence spectra, whereas mutant D63A and D195N showed higher intensity than wild-type. The amino acid sequence of wild-type LFTase was compared to the sequences of exo-inulinase from Aspergillus awamori, a plant fructan 1-exohydrolase from Cichorium intybus, and Thermotogo maritime (Tm) invertase and showed a high identity with Exo-inulinase from Aspergillus awamori.

• Proceedings of the Korea Crystallographic Association Conference
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• 2003.05a
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• pp.18-18
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• 2003

Thioredoxin (Trx) is a small redox protein that is ubiquitously distributed from achaes to human. In diverse organisms, the protein is involved in various physiological roles by acting as electron donor and regulators of transcription and apoptosis as well as antioxidants. Sequences of Trx within various species are 27～69% identical to that of E. coli and all Trx proteins have the same overall fold, which consists of central five β strands surrounded by four α helices. The N-terminal cysteine in WCGPC motif of Trx is redox sensitive and the motif is highly conserved. Compared with general cysteine, the N-terminal cysteine has low pKa value. The result leads to increased reduction activity of protein. Recently, novel thio.edoxin-related protein (TRP14) was found from rat brain. TRP14 acts as disulfide reductase like Trx1, and its redox potential and pKa are similar to those of Trx1. However, TRP14 takes up electrons from cytosolic thioredoxin reductase (TrxR1), not from the mitochondrial thioredoxin reductase (TrxR2). Biological roles of TES14 were reported to be involved in regulating TNF-α induced signaling pathways in different manner with Trx1. In depletion experiments, depletion of TRP14 increased TNF-α induced phosphorylation and degradation of IκBα more than the depletion Trx1 did. It also facilitated activation of JNK and p38 MAP kinase induced by TNF-α. Unlike Trx1, TRP14 shows neither interaction nor interference with ASK1. Here, we determined three-dimensional crystal structure of TRP14 by MAD method at 1.8Å. The structure reveals that the conserved cis-Pro (Pro90) and active site-W-C-X-X-C motif, which may be involved in substrate recognition similar to Trx1 , are located at the beginning position of strand β4 and helix α2, respectively. The TRP14 structure also shows that surface of TRP14 in the vicinity of the active site, which is surrounded by an extended flexible loop and an additional short a helix, is different from that of Trx1. In addition, the structure exhibits that TRP14 interact with a distinct target proteins compared with Trx1 and the binding may depend mainly on hydrophobic and charge interactions. Consequently, the structure supports biological data that the TRP14 is involved in regulating TNF-α induced signaling pathways in different manner with Trx1.