• 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.

• Journal of Microbiology and Biotechnology
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• v.30 no.9
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• pp.1436-1442
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• 2020

Amylosucrase (ASase, E.C. 2.4.1.4) is capable of efficient glucose transfer from sucrose, acting as the sole donor molecule, to various functional acceptor compounds, such as polyphenols and flavonoids. An ASase variant from Deinococcus geothermalis, in which the 226^th alanine is replaced with asparagine (DgAS-A226N), shows increased polymerization activity due to changes in the flexibility of the loop near the active site. In this study, we further investigated how the mutation modulates the enzymatic activity of DgAS using molecular dynamics and docking simulations to evaluate interactions between the enzyme and phenolic compounds. The computational analysis revealed that the A226N mutation could induce and stabilize structural changes near the substrate-binding site to increase glucose transfer efficiency to phenolic compounds. Kinetic parameters of DgAS-A226N and WT DgAS were determined with sucrose and 4-methylumbelliferone (MU) as donor and acceptor molecules, respectively. The k_cat/K_m value of DgAS-A226N with MU (6.352 mM^-1min^-1) was significantly higher than that of DgAS (5.296 mM^-1min^-1). The enzymatic activity was tested with a small phenolic compound, hydroquinone, and there was a 1.4-fold increase in α-arbutin production. From the results of the study, it was concluded that DgAS-A226N has improved acceptor specificity toward small phenolic compounds by way of stabilizing the active conformation of these compounds.

• Genomics & Informatics
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• v.18 no.4
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• pp.42.1-42.9
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• 2020

Chromatin immunoprecipitation coupled with high-throughput DNA sequencing (ChIP-Seq) is a powerful technology to profile the location of proteins of interest on a whole-genome scale. To identify the enrichment location of proteins, many programs and algorithms have been proposed. However, none of the commonly used peak calling programs could accurately explain the binding features of target proteins detected by ChIP-Seq. Here, publicly available data on 12 histone modifications, including H3K4ac/me1/me2/me3, H3K9ac/me3, H3K27ac/me3, H3K36me3, H3K56ac, and H3K79me1/me2, generated from a human embryonic stem cell line (H1), were profiled with five peak callers (CisGenome, MACS1, MACS2, PeakSeq, and SISSRs). The performance of the peak calling programs was compared in terms of reproducibility between replicates, examination of enriched regions to variable sequencing depths, the specificity-to-noise signal, and sensitivity of peak prediction. There were no major differences among peak callers when analyzing point source histone modifications. The peak calling results from histone modifications with low fidelity, such as H3K4ac, H3K56ac, and H3K79me1/me2, showed low performance in all parameters, which indicates that their peak positions might not be located accurately. Our comparative results could provide a helpful guide to choose a suitable peak calling program for specific histone modifications.

• Journal of Veterinary Science
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• v.21 no.3
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• pp.35.1-35.11
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• 2020

Background: Despite common use of tylosin in turkeys, the pharmacokinetic (PK) data for this drug in turkeys is limited. Within a few months of growth, PK of drugs in turkeys undergoes changes that may decrease their efficacy due to variable internal exposure. Objectives: The objective of this study was to investigate the influence of age on the PK of a single intravenous (i.v.) and oral administration of tylosin to turkeys at a dose of 10 and 50 mg/kg, respectively. Methods: Plasma drug concentrations were measured using high-performance liquid chromatography with UV detection. The PK parameters were assessed by means of non-compartmental approach and were subjected to allometric analysis. Results: During a 2.5-month-long period of growth from 1.4 to 14.7 kg, the median value for area under the concentration-time curve after i.v. administration increased from 2.61 to 7.15 mg × h/L and the body clearance decreased from a median of 3.81 to 1.42 L/h/kg. Over the same time, the median elimination half-life increased from 1.03 to 2.96 h. For the oral administration a similar trend was noted but the differences were less pronounced. Bioavailability was variable (5.76%-21.59%) and age-independent. For both routes, the plasma concentration of the major tylosin metabolite, tylosin D, was minimal. Protein binding was age-independent and did not exceed 50%. Allometric analysis indicated a relatively poor predictivity of clearance, volume of distribution and elimination half-life for tylosin in turkeys. Conclusions: Age has a significant impact on tylosin PK in turkeys and dosage adjustment may be needed, particularly in young individuals.

• Biomolecules & Therapeutics
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• v.31 no.1
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• pp.82-88
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• 2023

Genomic analysis indicated that the genome of Drosophila melanogaster contains more than 80 cytochrome P450 genes. To date, the enzymatic activity of these P450s has not been extensively studied. Here, the biochemical properties of CYP6A8 were characterized. CYP6A8 was cloned into the pCW vector, and its recombinant enzyme was expressed in Escherichia coli and purified using Ni²⁺-nitrilotriacetate affinity chromatography. Its expression level was approximately 130 nmol per liter of culture. Purified CYP6A8 exhibited a low-spin state in the absolute spectra of the ferric forms. Binding titration analysis indicated that lauric acid and capric acid produced type I spectral changes, with K_d values 28 ± 4 and 144 ± 20 µM, respectively. Ultra-performance liquid chromatography-mass spectrometry analysis showed that the oxidation reaction of lauric acid produced (ω-1)-hydroxylated lauric acid as a major product and ω-hydroxy-lauric acid as a minor product. Steady-state kinetic analysis of lauric acid hydroxylation yielded a k_cat value of 0.038 ± 0.002 min^-1 and a K_m value of 10 ± 2 µM. In addition, capric acid hydroxylation of CYP6A8 yielded kinetic parameters with a k_cat value of 0.135 ± 0.007 min^-1 and a K_m value of 21 ± 4 µM. Because of the importance of various lipids as carbon sources, the metabolic analysis of fatty acids using CYP6A8 in this study can provide an understanding of the biochemical roles of P450 enzymes in many insects, including Drosophila melanogaster.

• Computers and Concrete
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• v.31 no.2
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• pp.85-95
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• 2023

Natural pozzolans are used as additives in cement to develop more durable and high-performance concrete. Pozzolanic activity index (PAI) is important for assessing the performance of a pozzolan as a binding material and has an important effect on the compressive strength, permeability, and chemical durability of concrete mixtures. However, the determining of the 28 days (short term) and 90 days (long term) PAI of concrete mixtures is a time-consuming process. In this study, to reduce extensive experimental work, it is aimed to predict the short term and long term PAIs as a function of the chemical compositions of various natural pozzolans. For this purpose, the chemical compositions of various natural pozzolans from Central Anatolia were determined with X-ray fluorescence spectroscopy. The mortar samples were prepared with the natural pozzolans and then, the short term and the long term PAIs were calculated based on compressive strength method. The effect of the natural pozzolans' chemical compositions on the short term and the long term PAIs were evaluated and the PAIs were predicted by using multiple linear regression (MLR) and adaptive neuro-fuzzy inference system (ANFIS) model. The prediction model results show that both reactive SiO₂ and SiO₂+Al₂O₃+Fe₂O₃ contents are the most effective parameters on PAI. According to the performance of prediction models determined with metrics such as root mean squared error (RMSE) and coefficient of correlation (R²), ANFIS models are more feasible than the multiple regression model in predicting the 28 days and 90 days pozzolanic activity. Estimation of PAIs based on the chemical component of natural pozzolana with high-performance prediction models is going to make an important contribution to material engineering applications in terms of selection of favorable natural pozzolana and saving time from tedious test processes.

• Anatomy and Cell Biology
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• v.56 no.4
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• pp.518-525
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• 2023

Septin4 belong to a family of polymerizing GTP-binding proteins that are required for many cellular functions, such as membrane compartmentalization, vesicular trafficking, mitosis, and cytoskeletal remodeling. Since, Septin4 is expressed specifically in the testis, we aimed to determine the association between Septin4 gene expression with sperm quality, DNA damage, and stress oxidative level in infertile patients. The present study included 60 semen samples that grouped into three groups: normozoospermia (n=20), asthenozoospermia (n=20), astheno-teratozoospermia (n=20). Initially, semen parameters were analyzed by using the World Health Organization protocol. The mRNA expression of Septin4 in sperm was examined using reverse transcription-polymerase chain reaction. Oxidative stress markers, i.e., total antioxidant capacity, superoxide dismutase, catalase, glutathione peroxidase, and malondialdehyde, were determined by ELISA kit. The current study showed a statistically significant highly positive correlation in Septin4 gene expression with sperm motility, normal morphology, viability, capacity, and sperm mitochondrial membrane potential (MMP). However, it showed significant negative correlation with sperm DNA fragmentation. Septin4 had a significant correlation with stress oxidative factor and antioxidant enzyme levels. In conclusion, Septin4 gene expression provides clinical useful information for the diagnosis of male infertility. It might be a marker for discrimination between fertile and infertile patients. The current study showed a statistically significant highly positive correlation in Septin4 gene expression with sperm motility, normal morphology, viability, capacity, and sperm MMP. However, it shows significant negative correlation with sperm DNA fragmentation. Septin4 had a significant correlation with stress oxidative factor and antioxidant enzyme levels.

• The Korea Journal of Herbology
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• v.39 no.4
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• pp.19-28
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• 2024

Objectives : Ephedrae Herba has been used in the East Asian traditional medicine, for treatment of asthma, cold and influenza. Silymarin is an effective antioxidant and its anti-fibrogenic, anti-inflammatory, and hepatoprotective properties have been reported. This study was performed to explore an anti-fibrogenic potential of Ephedrae Herba extract (EHE) + silymarin on immortalized human hepatic stellate cell line, LX-2 cells. Methods : We studied the anti-fibrogenic effects of EHE + silymarin on transforming growth factor β1 (TGF-β1) signaling pathway in LX-2 cells. Cell viability was measured using the MTT assay. mRNA levels were detected by real-time PCR. TGF-β1 signaling-related proteins expression were detected by Western blot. Results : Silymarin 30 ㎍/mL and EHE 100 ㎍/mL showed cytotoxicity on LX-2 cells. Therefore, the concentrations of silymarin and EHE were studied at 10 ㎍/mL, respectively. Silymarin significantly reduced PAI-1 protein expression, Smad binding element (SBE) luciferase activity, and mRNA (PAI-1, MMP2 and 9) expression compared to TGF-β1. EHE significantly reduced SBE luciferase activity and mRNA (PAI-1, MMP2 and 9) expression compared to TGF-β1. More importantly, EHE + silymarin significantly reduced all parameters compared to TGF-β1, and also significantly reduced compared to EHE alone and silymarin alone. Conclusion : The results indicate that EHE + silymarin has anti-fibrogenic effect in LX-2 cells induced by TGF-β1. Additionally, EHE + silymarin shows more effective anti-fibrogenic effect than EHE alone and silymarin alone.

• Applied Chemistry for Engineering
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• v.7 no.3
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• pp.554-564
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• 1996

Oxygen reduction in an alkaline fuel cell was studied by using perovskite of $La_{0.6}Sr_{0.4}Co_{1-x}Fe_xO_3$(x=0.00, 0.01, 0.10, 0.20, 0.35, and 0.50) as an oxygen electrode catalyst. The changes in the catalytic properties as a function of Fe content were investigated by XRD, TG, and TPR. XRD patterns gave different lattice parameters of the catalysts. TG study revealed that Fe was so stabilized in the perovskite structure as to be hardly reduced even up to $900^{\circ}C$, and the amount of oxygen which was eliminated at high temperature increased with the fraction of Fe because Fe induced the increase of Co-O binding energy. From TPR study, ${\alpha}$-(low temperature peak) and ${\beta}$-(high temperature peak)states were observed. The bond strength of the ${\beta}$-species which was associated strongly with Co of the perovskite increased proportionally with the fraction of Fe. The ${\alpha}$-species, reversible oxygen, was the active species in the oxygen reduction. The ${\alpha}$-peak temperature which reflected the binding energy between Co and ${\alpha}$-state oxygen moved to lower temperature with the increase of lattice parameter of the catalytst due to the increase of Fe content. The decrease in the binding energy increased the activity in the oxygen reduction, but the decrease of ${\alpha}$-species with the increase of Fe content decreased the activity. The increase in the surface area with Fe content had little effect on the activity.

• Clinical and Experimental Pediatrics
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• v.51 no.7
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• pp.722-728
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• 2008

Purpose : This study was designed to examine the effects of adiponectin, leptin, insulin, insulin-like growth factor (IGF)-I and IGF binding protein (BP)-3 levels in cord blood on weight, length, and adiposity at birth in healthy term infants. In addition, we evaluated the mechanism to change the hormone levels in appropriate for gestational age (AGA) during the first month. Methods : We collected cord blood from 200 term neonates (109 males, 91 females) with no perinatal problems, and measured the hormone levels and anthropometric parameters including weight, length, and skin-fold thickness. Term neonates were divided into 3 groups as follows: birth weight appropriate for gestational age (AGA) (n=132), birth weight less for gestational age (SGA) (n=29), and birth weight more for gestational age (LGA) (n=39). Venous blood samples of 15 fullterm healthy neonates were obtained at 3, 7, and 30 d after birth. Results : The adiponectin, insulin, and IGF-I levels were significantly lower in the SGA group than in the AGA and LGA groups. The leptin levels were significantly higher in the LGA group than in the AGA and SGA groups. Cord blood adiponectin, leptin, insulin, IGF-I, and IGFBP-3 levels correlated significantly and positively with birth weight and the sum of the skin-fold thickness. A significant positive correlation was observed between adiponectin, leptin, and IGF-I levels and birth weight. Adiponectin level correlated significantly with that leptin level (r=0.191, P=0.038), but not with insulin, IGF-I and IGFBP-3 levels. IGF-I levels were higher in females than in males. At 7 d after birth, the leptin level decreased along with physiologic weight loss, and then increased. IGF-I, also decreased at 3 d, significantly increased 1 month later. Conclusion : We suggest that adiponectin, leptin, insulin, IGF-I, and IGFBP-3 play an important role in regulating fetal growth. Adiponectin may be involved in regulating fetal growth through mechanisms different from those mediated by insulin or IGF-I. High levels of IGF-I in female neonates indicates a gender difference which serves as evidence for in utero sexual dimorphism. It is likely that IGF-I has a more important role than that of hormones in postnatal growth.