• Asian Pacific Journal of Cancer Prevention
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• v.14 no.9
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• pp.5311-5316
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• 2013

A functional polymorphism in the NQO1 gene, featuring a 609C>T substitution,leading to proline to serine amino-acid and enzyme activity changes, has been implicated in cancer risk. However, individually published investigations showed inconclusive results, especially for leukemia. In this study, we therefore performed a meta-analysis of 21 publications with a total of 3,634 cases and 4,827controls, mainly for leukemia. We summarized the data on the association between the NQO1 609C>T polymorphism and risk of leukemia and performed subgroup analyses by ethnicity and leukemia type. We found that the variant TT homozygous genotype o was associated with a modestly increased risk of leukemia (TT versus CT/CC: OR=1.23, 95%CI=1.00-1.51, heterogeneity=0.76; $I^2$=0%). Following further stratified analyses, increased risk was only observed in subgroups of Caucasians. This meta-analysis suggests that the NQO1 609T allele is a high-penetrance risk factor for leukemia in Caucasians. The effect on leukemia may be modified by ethnicity and leukemia type, and the small sample sizes of the subgroup analyses suggest that further larger studies are needed.

• Journal of Microbiology and Biotechnology
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• v.25 no.1
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• pp.89-97
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• 2015

Bacillus subtilis HK176 with high fibrinolytic activity was isolated from cheonggukjang, a Korean fermented soyfood. A gene, aprE176, encoding the major fibrinolytic enzyme was cloned from B. subtilis HK176 and overexpressed in E. coli BL21(DE3) using plasmid pET26b(+). The specific activity of purified AprE176 was 216.8 ± 5.4 plasmin unit/mg protein and the optimum pH and temperature were pH 8.0 and 40℃, respectively. Error-prone PCR was performed for aprE176, and the PCR products were introduced into E. coli BL21(DE3) after ligation with pET26b(+). Mutants showing enhanced fibrinolytic activities were screened first using skim-milk plates and then fibrin plates. Among the mutants, M179 showed the highest activity on a fibrin plate and it had one amino acid substitution (A176T). The specific activity of M179 was 2.2-fold higher than that of the wild-type enzyme, but the catalytic efficiency (k_cat/K_m) of M179 was not different from the wild-type enzyme owing to reduced substrate affinity. Interestingly, M179 showed increased thermostability. M179 retained 36% of activity after 5 h at 45℃, whereas AprE176 retained only 11%. Molecular modeling analysis suggested that the 176^th residue of M179, threonine, was located near the cation-binding site compared with the wild type. This probably caused tight binding of M179 with Ca²⁺, whichincreased the thermostability of M179.

• Journal of Animal Science and Technology
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• v.47 no.2
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• pp.159-166
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• 2005

Porcine myostatin(MS1N) gene plays a key role in the differentiation of myoblast and muscle development. Genetic polymorphism was screened by single stranded conformation polymorphism(SSCP) analysis and subsequent DNA sequencing detected a nucleotide substitution(C2150T) in exon 3 of MSIN gene. Phenotypic association of the polymorphism was tested in a Landrace population and positive effects of the allele T for lean growth traits were found in the population. Even though it is not significant, the pigs have IT and TC genotypes were heavier for the body weight at birth and at twenty weeks of age than those containing genotype. Cc. However, the allele T was significantly associated with higher eye muscle area(P < 0.05). As a result of this study, we suggested that the allele T in exon 3 of MSTN gene comes a significant effect for increasing the eye muscle area without decreasing backfat thickness. This polymorphism did not change the amino acid but Taq I -RFLP matched to SSCP band patterns in exon 3 of MSTN gene, which will be an useful molecular marker for breeding of Landrace pigs.

• The Plant Pathology Journal
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• v.30 no.2
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• pp.195-199
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• 2014

Apple stem pitting virus (ASPV), of the Foveavirus genus in the family Betaflexiviridae, is one of the most common viruses of apple and pear trees. To examine variability of the coat protein (CP) gene from ASPV, eight isolates originating from 251 apple trees, which were collected from 22 apple orchards located in intensive apple growing areas of the North Gyeongsang and North Jeolla Provinces in Korea, were sequenced and compared. The nucleotide sequence identity of the CP gene of eight ASPV isolates ranged from 77.0 to 97.0%, while the amino acid sequence identity ranged from 87.7 to 98.5%. The N-terminal region of the viral CP gene was highly variable, whereas the C-terminal region was conserved. Genetic algorithm recombination detection (GARD) and single breakpoint recombination (SBP) analyses identified base substitutions between eight ASPV isolates at positions 54 and 57 and position 771, respectively. GABranch analysis was used to determine whether the eight isolates evolved due to positive selection. All values in the GABranch analysis showed a ratio of substitution rates at non-synonymous and synonymous sites (dNS/dS) below 1, suggestive of strong negative selection forces during ASPV CP history. Although negative selection dominated CP evolution in the eight ASPV isolates, SLAC and FEL tests identified four possible positive selection sites at codons 10, 22, 102, and 158. This is the first study of the ASPV genome in Korea.

• Bulletin of the Korean Chemical Society
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• v.30 no.6
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• pp.1360-1364
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• 2009

The bacterium Sphingomonas chungbukensis DJ77 produces the extracellular polysaccharide gellan in high yield. Gellan produced by this bacterium is widely used as a gelling agent, and the enzyme UDP-glucose pyrophosphorylase (UGP) is thought to play a key role in the gellan biosynthetic pathway. The UGP gene has been successfully cloned and over-expressed in E. coli. The expressed enzyme was purified with a molecular weight of approximately 32 kDa, as determined by a SDS-polyacrylamide gel, but the enzyme appears as ca. 63 kDa on a native gel, suggesting that the enzyme is present in a homodimer. Kinetic analysis of UDP-glucose for UGP indicates $K_m$ = 1.14 mM and $V_{max}$ = 10.09 mM/min/mg at pH 8.0, which was determined to be the optimal pH for UGP catalytic activity. Amino acid sequence alignment against other bacteria suggests that the UGP contains two conserved domains: An activator binding site and a glucose-1-phosphate binding site. Site-directed mutagenesis of Lys194, located within the glucose-1-phosphate binding site, indicates that substitution of the charge-reversible residue Asp for Lys194 dramatically impairs the UGP activity, supporting the hypothesis that Lys194 plays a critical role in the catalysis.

• Journal of Microbiology and Biotechnology
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• v.23 no.1
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• pp.7-14
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• 2013

In the Bacillus amyloliquefaciens ${\alpha}$-amylase (BAA), the loop (residues 176-185; region I) that is the part of the calcium-binding site (CaI, II) has two more amino acid residues than the ${\alpha}$-amylase from Bacillus licheniformis (BLA). Arg176 in this region makes an ionic interaction with Glu126 from region II (residues 118-130), but this interaction is lost in BLA owing to substitution of R176Q and E126V. The goal of the present work was to quantitatively estimate the effect of ionic interaction on the overall stability of the enzyme. To clarify the functional and structural significance of the corresponding salt bridge, Glu126 was deleted (${\Delta}$E126) and converted to Val (E126V), Asp (E126D), and Lys (E126K) by site-directed mutagenesis. Kinetic constants, thermodynamic parameters, and structural changes were examined for the wild-type and mutated forms using UV-visible, atomic absoption, and fluorescence emission spectroscopy. Wild-type exhibited higher $k_{cat}$ and $K_m$ but lower catalytic efficiency than the mutant enzymes. A decreased thermostability and an increased flexibility were also found in all of the mutant enzymes when compared with the wild-type. Additionally, the calcium content of the wild-type was more than ${\Delta}E126$. Thus, it may be suggested that ionic interaction could decrease the mobility of the discussed region, prevent the diffusion of cations, and improve the thermostability of the whole enzyme. Based on these observations, the contribution of loop destabilization may be compensated by the formation of a salt bridge that has been used as an evolutionary mechanism or structural adaptation by the mesophilic enzyme.

• Plant Biotechnology Reports
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• v.2 no.1
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• pp.75-85
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• 2008

Prune dwarf virus (PDV) is an Ilarvirus systemically infecting almond trees and other Prunus species and spreading through pollen, among other means. We have studied strategies based on coat protein (cp) gene to block PDV replication in host plant cells. A Portuguese isolate of PDV was obtained from infected almond leaves and used to produce the cDNA of the cp gene. Various constructs were prepared based on this sequence, aiming for the transgenic expression of the original or modified PDV coat protein (cpPDVSense and cpPDVMutated) or for the expression of cpPDV RNA (cpPDVAntisense and cpPDVwithout start codon). All constructs were tested in a PDV host model, Nicotiana benthamiana, and extensive molecular characterization and controlled infections were performed on transformants and their progenies. Transgenic plants expressing the coat protein RNA were able to block the proliferation of a PDV isolate sharing only 91% homology with the isolate used for cpPDV cloning, as evaluated by DAS-ELISA on newly developed leaves. With cp expression, the blockage of PDV proliferation in newly developed leaves was only achieved with the construct cpPDV Mutated, where the coat protein has a substitution in the 14th aa residue, with arginine replaced by alanine. This result points to a possible role of the mutated amino acid in the virus ability to replicate and proliferate. This work reveals the possibility of achieving protection against PDV through either coat protein RNA or mutated cp sequence.

• Journal of Ginseng Research
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• v.48 no.1
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• pp.89-97
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• 2024

Background: Ginsenoside F2 (GF2), the protopanaxadiol-type constituent in Panax ginseng, has been reported to attenuate metabolic dysfunction-associated steatotic liver disease (MASLD). However, the mechanism of action is not fully understood. Here, this study investigates the molecular mechanism by which GF2 regulates MASLD progression through liver X receptor (LXR). Methods: To demonstrate the effect of GF2 on LXR activity, computational modeling of protein-ligand binding, Time-resolved fluorescence resonance energy transfer (TR-FRET) assay for LXR cofactor recruitment, and luciferase reporter assay were performed. LXR agonist T0901317 was used for LXR activation in hepatocytes and macrophages. MASLD was induced by high-fat diet (HFD) feeding with or without GF2 administration in WT and LXRα^-/- mice. Results: Computational modeling showed that GF2 had a high affinity with LXRα. LXRE-luciferase reporter assay with amino acid substitution at the predicted ligand binding site revealed that the S264 residue of LXRα was the crucial interaction site of GF2. TR-FRET assay demonstrated that GF2 suppressed LXRα activity by favoring the binding of corepressors to LXRα while inhibiting the accessibility of coactivators. In vitro, GF2 treatments reduced T0901317-induced fat accumulation and pro-inflammatory cytokine expression in hepatocytes and macrophages, respectively. Consistently, GF2 administration ameliorated hepatic steatohepatitis and improved glucose or insulin tolerance in WT but not in LXRα^-/- mice. Conclusion: GF2 alters the binding affinities of LXRα coregulators, thereby interrupting hepatic steatosis and inflammation in macrophages. Therefore, we propose that GF2 might be a potential therapeutic agent for the intervention in patients with MASLD.

• Korean Journal of Agricultural Science
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• v.37 no.3
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• pp.399-404
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• 2010

Single nucleotide polymorphisms (SNPs) in chicken lysozyme (LYZ) gene were investigated in this study. The identification of SNPs in both exon and intron in LYZ gene has led to understanding of evolution for the domestic chicken populations. A total of 24 samples from two Korean native commercial chicken populations (CCPs) were used for the initial identification of SNPs by mixing three DNA samples for sequencing experiments. By comparing with red jungle fowl (RJF), two commercial chicken populations have 18 common polymorphisms. Between two commercial chicken populations, 15 polymorphisms were identified. Of the 33 polymorphisms identified, two indels (21 and 4 bp) were found. Whereas, only one polymorphism in exon 2 at the bp position 1426 was a non-synonymous substitution (p.Ala49Val), indicating the amino acid changes. The identified non-synonymous substitution (p.Ala49Val) is located close to the catalytic sites of the enzyme, which might affect its activity. In our investigation, the polymorphisms in LYZ gene can provide broad ideas for the variation of Korean native chicken populations from the ancestor of chicken breeds as well as the some biological functions of the LYZ gene.

• Asian-Australasian Journal of Animal Sciences
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• v.32 no.4
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• pp.564-573
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• 2019

Objective: Evaluate the effects of i) dehulling of lupine seed on chemical composition and apparent metabolizable energy (AME) and ii) soybean meal substitution by dehulled lupine seed in broiler diets with enzymes on productive performance, size of digestive organs and welfare-related variables. Methods: Experiment 1, chemical composition and AME were determined in whole and dehulled lupine seed. Experiment 2, two hundred eighty-eight one-day-old male Ross 308 broilers were used. The experimental diets were maize-soybean meal (MS), MS with enzymes (MSE) and maize-dehulled lupine seed with enzymes (MLE). Diets were assigned to the experimental units under a completely randomized design (eight replicates per diet). The body weight (BW) gain, feed intake, feed conversion, digestive organ weights, gait score, latency to lie down and valgus/varus angulation were evaluated. Results: The dehulling process increased protein (25.0% to 31.1%), AME (5.9 to 8.8 MJ/kg) and amino acid contents. The BW gain of broilers fed the MLE diet was similar (p>0.05) to that of those fed the MS diet, but lower than that of those fed the MSE diet. Feed intake of broilers fed the MLE diet was higher (p<0.05) than that of those fed the MS diet and similar (p>0.05) to those fed the MSE diet. Feed conversion of broilers fed the MLE diet was 8.0% and 8.7% higher (p<0.05) than that of those fed the MS and MSE diets, respectively. Broilers fed the MLE diet had the highest (p<0.05) relative proventriculus and gizzard weights, but had poor welfare-related variables. Conclusion: It is possible to substitute soybean meal by dehulled lupine seed with enzymes in broiler diets, obtaining similar BW gains in broilers fed the MLE and MS diets; however, a higher feed intake is required. Additionally, the MLE diet reduced welfare-related variables.