• BMB Reports
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• v.40 no.5
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• pp.697-707
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• 2007

Cytochrome $cbb_3$ oxidase is a member of the heme-copper oxidase superfamily that catalyses the reduction of molecular oxygen to the water and conserves the liberated energy in the form of a proton gradient. Comparison of the amino acid sequences of subunit I from different classes of heme-copper oxidases showed that transmembrane helix VIII and the loop between transmembrane helices IX and X contain five highly conserved polar residues; Ser333, Ser340, Thr350, Asn390 and Thr394. To determine the relationship between these conserved amino acids and the activity and assembly of the $cbb_3$ oxidase in Rhodobacter capsulatus, each of these five conserved amino acids was substituted for alanine by site-directed mutagenesis. The effects of these mutations on catalytic activity were determined using a NADI plate assay and by measurements of the rate of oxygen consumption. The consequence of these mutations for the structural integrity of the $cbb_3$ oxidase was determined by SDS-PAGE analysis of chromatophore membranes followed by TMBZ staining. The results indicate that the Asn390Ala mutation led to a complete loss of enzyme activity and that the Ser333Ala mutation decreased the activity significantly. The remaining mutants cause a partial loss of catalytic activity. All of the mutant enzymes, except Asn390Ala, were apparently correctly assembled and stable in the membrane of the R. capsulatus.

• Membrane and Water Treatment
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• v.7 no.3
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• pp.175-191
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• 2016

In this work, oil-in-water emulsions (O/W) were prepared successfully by membrane emulsification with $0.5{\mu}m$ pore size membrane. Sunflower oil was emulsified in aqueous Tween80 solution with a simple crossflow apparatus equipped with ceramic tube membrane. In order to increase the shear-stress near the membrane wall, a helical-shaped reducer was installed within the lumen side of the tube membrane. This method allows the reduction of continuous phase flow and the increase of dispersed phase flux, for cost effective production. Results were compared with the conventional cross-flow membrane emulsification method. Monodisperse O/W emulsions were obtained using tubular membrane with droplet size in the range $3.3-4.6{\mu}m$ corresponded to the membrane pore diameter of $0.5{\mu}m$. The final aim of this study is to obtain O/W emulsions by simple membrane emulsification method without reducer and compare the results obtained by membrane equipped with helix shaped reducer. To indicate the results statistical methods, $3^p$ type full factorial experimental designs were evaluated, using software called STATISTICA. For prediction of the flux, droplet size and PDI a mathematical model was set up which can describe well the dependent variables in the studied range, namely the run of the flux and the mean droplet diameter and the effects of operating parameters. The results suggested that polynomial model is adequate for representation of selected responses.

• Biotechnology and Bioprocess Engineering:BBE
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• v.10 no.4
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• pp.289-295
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• 2005

In this study, the cultural medium used for the efficient production of $\gamma$-PGA with a newly isolated Bacillus sp. RKY3 was optimized. It was necessary to supplement the culture medium with L-glutamic acid and an additional carbon source in order to induce the effective production of $\gamma$-PGA. The amount of $\gamma$-PGA increased with the addition of L-glutamic acid to the medium. The addition of 90 g/L L-glutamic acid to the medium resulted in the maximal yield of $\gamma$-PGA (83.2 g/L). The optimum nitrogen source was determined to be peptone, but corn steep liquor, a cheap nutrient, was also found to be effective for $\gamma$-PGA production. Both the $\gamma$-PGA production and cell growth increased rapidly with the addition of small amounts of $K_2HPO_4$ and $MgSO_4\cdot7H_{2}O$. Bacillus sp. RKY3 appears to require $Mg^{2+}$, rather than $Mn^{2+}$, for $\gamma$-PGA production, which is distinct from the production protocols associated with other, previously reported bacteria. Bacillus sp. RKY3 may also have contributed some minor $\gamma$-PGA depolymerase activity, resulting in the reduction of the molecular weight of the produced $\gamma$-PGA at the end of fermentation.

• BMB Reports
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• v.43 no.8
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• pp.547-553
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• 2010

Biochemical tests such as aspartate aminotransferase (AST) and alanine aminotransferase (ALT) are useful for diagnosing patients with liver disease. In this study, we tested the association between copy number variation and the hepatic biomarkers AST and ALT based on 8,842 samples from population-based cohorts in Korea. We used Affymetrix Genome-Wide Human 5.0 arrays and identified 10,534 CNVs using HelixTree software. Of the CNVs tested using univariate linear regression, 100 CNVs were significant for AST and 16 were significant for ALT (P < 0.05). We identified 39 genes located within the CNV regions. DKK1 and HS3ST3B1 were shown to play roles in heparan sulfate biosynthesis and the Wnt signaling pathway, respectively. NAF1 and NPY1R were associated with glycoprotein processes and neuropeptide Y receptor activity based on GO categories. PTER, SOX14 and TM7SF4 were expressed in liver. DPYS and CTSC were found to be associated with dihydropyrimidinuria and Papillon-Lefevre syndrome phenotypes using OMIM. NPY5R was found to be associated with dyslipidemia using the Genetic Association Database.

• Archives of Craniofacial Surgery
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• v.24 no.1
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• pp.18-23
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• 2023

Background: When performing reduction of zygomatic arch fractures, locating the inward portion of the fracture can be difficult. Therefore, this study investigated the discrepancy between the locations of the depression on the soft tissue and bone and sought to identify how to determine the inward portion of the fracture on the patient's face. Methods: We conducted a retrospective review of chart with isolated zygomatic arch fractures of type V in the Nam and Jung classification from March 2013 to February 2022. For consistent measurements, a reference point (RP), at the intersection between a vertical line passing through the end point of the root of the ear helix in the patient's side-view photograph and a transverse line passing through the longest horizontal axis of the external meatus opening, was established. We then measured the distance between the RP and the soft tissue depression in a portrait and the bone depression on a computed tomography (CT) scan. The discrepancy between these distances was quantified. Results: Among the patients with isolated zygomatic arch fractures, only those with a fully visible ear on a side-view photograph were included. Twenty-four patients met the inclusion criteria. There were four types of discrepancies in the location of the soft tissue depression compared to the bone depression: type I, forward and upward discrepancy (7.45 and 3.28 mm), type II, backward and upward (4.29 and 4.21 mm), type III, forward and downward (10.06 and 5.15 mm), and type IV, backward and downward (2.61 and 3.27 mm). Conclusion: This study showed that discrepancy between the locations of the depressions on the soft tissue and bone exists in various directions. Therefore, applying the transverse and vertical distances measured from a bone image of the CT scan onto the patient's face at the indicated RP will be helpful for predicting the reduction location.

• BMB Reports
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• v.40 no.3
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• pp.412-418
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• 2007

Phospholipid hydroperoxide glutathione peroxidase (PHGPx) is an unique antioxidant enzyme that directly reduces lipid hydroperoxides in biomembranes. In the present work, the entire encoding region for Oryza sativa PHGPx was expressed in Escherichia coli M15, and the purified fusion protein showed a single band with 21.0 kD and pI = 8.5 on SDS- and IFE-PAGE, respectively. Judging from CD and fluorescence spectroscopy, this protein is considered to have a well-ordered structure with 12.2% $\alpha$-helix, 30.7%$\beta$-sheet, 18.5% $\delta$-turn, and 38.5% random coil. The optimum pH and temperature of the enzyme activity were pH 9.3 and 27$^{\circ}C$. The enzyme exhibited the highest affinity and catalytical efficiency to phospholipid hydroperoxide employing GSH or Trx as electron donor. Moreover, the protein displayed higher GSH-dependent activity towards t-Butyl-OOH and $H_2O_2$. These results show that OsPHGPx is an enzyme with broad specificity for hydroperoxide substrates and yielded significant insight into the physicochemical properties and the dynamics of OsPHGPx.

• International Journal of Oral Biology
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• v.39 no.4
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• pp.169-176
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• 2014

A positional scanning synthetic peptide combinatorial library (PS-SCL) was screened in order to identify antimicrobial peptides against the cariogenic oral bacteria, Streptococcus mutans. Activity against Streptococcus gordonii and Aggregatibacter actinomycetemcomitans was also examined. The library was comprised of six sub-libraries with the format $O_{(1-6)}XXXXX-NH_2$, where O represents one of 19 amino acids (excluding cysteine) and X represents equimolar mixture of these. Each sub-library was tested for antimicrobial activity against S. mutans and evaluated for antimicrobial activity against S. gordonii and A. actinomycetemcomitans. The effect of peptides was observed using transmission electron microscopy (TEM). Two semi-mixture peptides, RXXXXN-$NH_2$ (pep-1) and WXXXXN-$NH_2$ (pep-2), and one positioned peptide, RRRWRN-$NH_2$ (pep-3), were identified. Pep-1 and pep-2 showed significant antimicrobial activity against Gram positive bacteria (S. mutans and S. gordonii), but not against Gram negative bacteria (A. actinomycetemcomitans). However, pep-3 showed very low antimicrobial activity against all three bacteria. Pep-3 did not form an amphiphilic ${\alpha}$-helix, which is a required structure for most antimicrobial peptides. Pep-1 and pep-2 were able to disrupt the membrane of S. mutans. Small libraries of biochemically-constrained peptides can be used to generate antimicrobial peptides against S. mutans and other oral microbes. Peptides derived from such libraries may be candidate antimicrobial agents for the treatment of oral microorganisms.

• Horticultural Science & Technology
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• v.34 no.1
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• pp.46-54
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• 2016

2-Oxoglutarate (2OG) acts as a signaling molecule and plays a critical role in secondary metabolism in a variety of organisms, including plants. Six 2-oxoglutarate (2OG) and Fe(II) oxygenase (2OGO) genes, VlCE2OGO1 [Vitis labruscana 2-oxoglutarate (2OG) and Fe(II) oxygenase 1], VlCE2OGO2, VlCE2OGO3, VlCE2OGO4, VlCE2OGO5, and VlCE2OGO6, which show different expression patterns upon transcriptome analysis of 'Campbell Early' grapevine exposed to low temperature for 4 weeks, were analyzed for their structure and expression. Comparison of the deduced amino acid sequences of the 2OGO genes from the V. labruscana transcripts revealed sequence similarities of 38.6% (VlCE2OGO1 and VlCE2OGO2) to 19.2% (VlCE2OGO2 and VlCE2OGO3). The lengths of these genes ranged from 1053 to 2298 bp, and they encoded 316 to 380 amino acids. The prediction of the secondary structure of the encoded proteins by Self-Optimized Prediction Method with Alignment (SOPMA) indicated that all the genes contained alpha helix (23.95 to 41.71%), extended strand (16 to 22.34%), beta turn (6.65 to 9.22%), and random coil (32.97 to 51.58%) in the analysis. Specific primers from unique regions in each gene obtained by alignment of nucleotide sequences were used in real time PCR for analysis of gene expression. All tested genes showed differential expression in grapevines exposed to low temperature. Of the six transcripts, VlCE2OGO1, VlCE2OGO2, and VlCE2OGO3 were up-regulated and VlCE2OGO4, VlCE2OGO5, and VlCE2OGO6 were down-regulated in response to cold treatments at all tested time points. The 2OG genes can be used for elucidation of mechanisms of tolerance to cold and as valuable molecular genetic resources for selection in breeding programs for cold-hardy grapevines.

• Journal of Contemporary Eastern Asia
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• v.18 no.1
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• pp.7-29
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• 2019

This study describes an approach for comparative bibliometric analysis of scientific publications related to (i) individual or several departments comprising a university, and (ii) broader integrated subject areas using multiple disciplinary schemes. It uses a custom dataset of scientific publications (ca. 15,000 articles and reviews, published during 2009-2013, and recorded in the Web of Science Core Collections) with author affiliations to the research departments, dedicated to science, technology, engineering, mathematics, and medicine (STEMM), of a comprehensive university. The dataset was subjected, at first, to the department level and discipline level analyses using the newly available KAKEN-L3 classification (based on MEXT/JSPS Grants-in-Aid system), hierarchical clustering, correspondence analysis to decipher the major departmental and disciplinary clusters, and visualization of the department-discipline relationships using two-dimensional stacked bar diagrams. The next step involved the creation of subsets covering integrated subject areas and a comparative analysis of departmental contributions to a specific area (medical, health and life science) using several disciplinary schemes: Essential Science Indicators (ESI) 22 research fields, SCOPUS 27 subject areas, OECD Frascati 38 subordinate research fields, and KAKEN-L3 66 subject categories. To illustrate the effective use of the science mapping techniques, the same subset for medical, health and life science area was subjected to network analyses for co-occurrences of keywords, bibliographic coupling of the publication sources, and co-citation of sources in the reference lists. The science mapping approach demonstrates the ways to extract information on the prolific research themes, the most frequently used journals for publishing research findings, and the knowledge base underlying the research activities covered by the publications concerned.

• Bulletin of the Korean Chemical Society
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• v.26 no.11
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• pp.1728-1734
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• 2005

The interactions of Cu(II)-meso-Tetrakis(n-N-methylpyridiniumyl)porphyrin (n = 2,3,4), respectively referred to as o-, m- and p-CuTMPyP, and DNA, poly$[d(A-T)_2]$ and poly$[d(G-C)_2]$ were investigated by circular and linear dichroism (CD and LD). In the o-CuTMPyP case, in which the rotation of the pyridinium ring is prevented, the shape of the CD spectrum when associated to DNA and poly$[d(A-T)_2]$ resembles and is characterized by a positive band at a low drug to DNA concentration ratio (R ratio) and is bisignate at a high R ratio. The former CD spectrum shape has been attributed to porphyrin that is bound monomerically outside of DNA while the latter can be attributed to those that are stacked. When o-CuTMPyP is bound to poly$[d(G-C)_2]$, the excitonic CD appeared at a relatively high R ratio. In contrast, a characteristic negative CD band in the Soret region was apparent for both m- and p-CuTMPyP when bound to DNA and poly$[d(G-C)_2]$ at the low R ratios, indicating that the porphyrin molecule intercalates. However, the DNA is bent near the intercalation site and the plane of the porphyrin molecule tilts relative to the DNA helix axis, as judged by the magnitude of the reduced LD. Various stacking patterns were identified by the shape of the CD spectrum for m- and p-CuTMPyP when bound to poly$[d(A-T)_2]$. Three species for the former complex and two for the latter complex were found which may reflect the extent of the stacking.