• The Journal of Korean Academy of Prosthodontics
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• v.42 no.3
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• pp.307-326
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• 2004

Statement of problem. The long-term success of implants is the development of a stable direct connection between bone and implant surface, which must be structural and functional. To improve a direct implant fixation to the bone, various strategies have been developed focusing on the surface of materials. Among them, altering the surface properties can modify cellular responses such as cell adhesion, cell motility and bone deposition. Purpose. This study was to evaluate the cellular behaviors on the surface-modified titanium by morphological observation, cellular proliferation and differentiation. Material and methods. Specimens were divided into five groups, depending on their surface treatment: electropolishing(EP) anoclizing(AN), machining(MA), blasting with hydroxyapatite particle(RBM) and electrical discharge machining(EDM). Physicochemical properties and microstructures of the specimens were examined and the responses of osteoblast-like cells were investigated. The microtopography of specimens was observed by scanning electron microscopy(SEM). Surface roughness was measured by a three-dimensional roughness measuring system. The microstructure was analyzed by X-ray diffractometer(XRD) and scanning auger electron microscopy(AES). To evaluate cellular responses to modified titanium surfaces, osteoblasts isolated from neonatal rat were cultured. The cellular morphology and total protein amounts of osteoblast-like cell were taken as the marker for cellular proliferation, while the expression of alkaline phosphatase was used as the early differentiation marker for osteoblast. In addition, the type I collagen production was determined to be a reliable indicator of bone matrix synthesis. Results. 1. Each prepared specimen showed specific microtopography at SEM examination. The RBM group had a rough and irregular pattern with reticulated appearance. The EDM-treated surface had evident cracks and was heterogeneous consisting of broad sheet or plate with smooth edges and clusters of small grains, deep pores or craters. 2. Surface roughness values were, from the lowest to the highest, electropolished group, anodized group, machined group, RBM group and EDM group. 3. All groups showed amorphous structures. Especially anodized group was found to have increased surface oxide thickness and EDM group had titaniumcarbide(TiC) structure. 4. Cells on electropolished, anodized and machined surfaces developed flattened cell shape and cells on RBM appeared spherical and EDM showed both. After 14 days, the cells cultured from all groups were formed to be confluent and exhibited multilayer proliferation, often overlapped or stratified. 5. Total protein amounts were formed to be quite similar among all the group at 48 hours. At 14 days, the electropolished group and the anodized group induced more total protein amount than the RBM group(P<.05). 6. There was no significant difference among five groups for alkaline phosphatase(ALP) activity at 48 hours. The AN group showed significantly higher ALP activity than any other groups at 14 days(P<.05). 7. All the groups showed similar collagen synthesis except the EDM group. The amount of collagen on the electropolished and anodized surfaces were higher than that on the EDM surface(P<.05).

• Molecules and Cells
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• v.24 no.3
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• pp.316-322
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• 2007

Glutaredoxins (Grxs), also known as thioltransferases (TTases), are thiol oxidoreductases that regulate cellular redox state in a variety of organisms. In the budding yeast Saccharomyces cerevisiae, Grx1 and 2 are cytosolic dithiol Grxs, while Grx3, 4 and 5 are monothiol Grxs. A gene encoding a new monothiol Grx, Grx6, was cloned from the genomic DNA of S. cerevisiae by PCR. Its DNA sequence contains 1,080 bp, and encodes a putative protein of 203 amino acid residues containing Cys-Phe-Tyr-Ser at the active site. Grx6 is similar to other monothiol Grxs in the same organism and to Grx3 in the fission yeast Schizosaccharomyces pombe. and its predicted three-dimensional structure resembles that of S. pombe Grx3. S. pombe cells harboring plasmid pFGRX6 containing the Grx6 gene had about 1.3-fold elevated Grx activity in the exponential phase, and grew better than the control cells under some stressful conditions. Synthesis of ${\beta}$-galactosidase from a Grx6-lacZ fusion gene in S. pombe was enhanced by potassium chloride, aluminum chloride and heat ($37^{\circ}C$) treatment. S. pombe cells harboring plasmid pFGRX6 had elevated ROS levels whereas S. pombe cells harboring extra copies of Grx3 had reduced ROS levels.

• Korean Journal of Poultry Science
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• v.45 no.3
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• pp.209-217
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• 2018

The innate immune recognition is based on the detection of microbial products. Toll-like receptors (TLRs) located on the cell surface and the endosome senses microbial components and nucleic acids, respectively. Chicken TLRs mediate immune responses by sensing ligands from pathogens, have been studied as immune adjuvants to increase the efficacy of vaccines. Single nucleotide polymorphisms (SNPs) of TLR3 and TLR4 genes in chicken were associated with resistance and susceptibility to viral infection. In this study, SNPs of chTLR3 and chTLR4 genes were retrieved from public database and annotated with chicken reference genome. Three-dimensional models of the chTLR3 and chTLR4 proteins were built using a Swiss modeler. We identified 35 and 13 nsSNPs in chTLR3 and chTLR4 genes respectively. Sorting Intolerant from Tolerant (SIFT) and Polymorphism Phenotyping v2 (Polyphen-2) analyses, suggested that, out of 35 and 13 nsSNPs, 4 and 2 SNPs were identified to be deleterious in chTLR3 and chTLR4 gene respectively. In chTLR3, 1 deleterious SNP was located in ectodomain and 3 were located in the Toll / IL-1 receptor (TIR) domain. Further structural model of chTLR3-TIR domain suggested that 1 deleterious SNP be present in the B-B loop region, which is important for TIR-TIR domain interactions in the downstream signaling. In chTLR4, the deleterious SNPs were located both in the ectodomain and TIR domain. SNPs predicted for chTLR3 and chTLR4 in this study, might be related to resistance or susceptible to viral infection in chickens. Results from this study will be useful to develop the effective measures in chicken against infectious diseases.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2003.10a
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• pp.1-1
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• 2003

It is clear that computers will play a key role in the biology of the future. Even now, it is virtually impossible to keep track of the key proteins, their names and associated gene names, physical constants(e.g. binding constants, reaction constants, etc.), and hewn physical and genetic interactions without computational assistance. In this sense, computers act as an auxiliary brain, allowing one to keep track of thousands of complex molecules and their interactions. With the advent of gene expression array technology, many experiments are simply impossible without this computer assistance. In the future, as we seek to integrate the reductionist description of life provided by genomic sequencing into complex and sophisticated models of living systems, computers will play an increasingly important role in both analyzing data and generating experimentally testable hypotheses. The future of bioinformatics is thus being driven by potent technological and scientific forces. On the technological side, new experimental technologies such as microarrays, protein arrays, high-throughput expression and three-dimensional structure determination prove rapidly increasing amounts of detailed experimental information on a genomic scale. On the computational side, faster computers, ubiquitous computing systems, high-speed networks provide a powerful but rapidly changing environment of potentially immense power. The challenges we face are enormous: How do we create stable data resources when both the science and computational technology change rapidly? How do integrate and synthesize information from many disparate subdisciplines, each with their own vocabulary and viewpoint? How do we 'liberate' the scientific literature so that it can be incorporated into electronic resources? How do we take advantage of advances in computing and networking to build the international infrastructure needed to support a complete understanding of biological systems. The seeds to the solutions of these problems exist, at least partially, today. These solutions emphasize ubiquitous high-speed computation, database interoperation, federation, and integration, and the development of research networks that capture scientific knowledge rather than just the ABCs of genomic sequence. 1 will discuss a number of these solutions, with examples from existing resources, as well as area where solutions do not currently exist with a view to defining what bioinformatics and biology will look like in the future.

• Journal of Microbiology and Biotechnology
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• v.24 no.7
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• pp.925-935
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• 2014

A cold-adapted carbohydrate esterase, CEST, belonging to the carbohydrate esterase family 6, was cloned from Microbulbifer thermotolerans DAU221. CEST was composed of 307 amino acids with the first 22 serving as a secretion signal peptide. The calculated molecular mass and isoelectric point of the mature enzyme were 31,244 Da and pH 5.89, respectively. The catalytic triad consisted of residues Ser37, Glu192, and His281 in the conserved regions: GQSNMXG, QGEX(D/N), and DXXH. The three-dimensional structure of CEST revealed that CEST belongs to the ${\alpha}/{\beta}$-class of protein consisted of a central six-stranded ${\beta}$-sheet flanked by eight ${\alpha}$-helices. The recombinant CEST was purified by His-tag affinity chromatography and the characterization showed its optimal temperature and pH were $15^{\circ}C$ and 8.0, respectively. Specifically, CEST maintained up to 70% of its enzyme activity when preincubated at $50^{\circ}C$ or $60^{\circ}C$ for 6 h, and 89% of its enzyme activity when preincubated at $70^{\circ}C$ for 1 h. The results suggest CEST belongs to group 3 of the cold-adapted enzymes. The enzyme activity was increased by $Na^+$ and $Mg^{2+}$ ions but was strongly inhibited by $Cu^+$ and $Hg^{2+}$ ions, at all ion concentrations. Using p-nitrophenyl acetate as a substrate, the enzyme had a $K_m$ of 0.278 mM and a $k_{cat}$ of $1.9s^{-1}$. Site-directed mutagenesis indicated that the catalytic triad (Ser37, Glu192, and His281) and Asp278 were essential for the enzyme activity.

• International Journal of Industrial Entomology and Biomaterials
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• v.9 no.2
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• pp.217-223
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• 2004

A cathepsin L-like cysteine protease, v-cath, encoded by the baculovirus has been shown to playa role in host liquefaction. We have identified a v-cath gene in the silkworm virus, Bombyx mori nuclear polyhedrosis virus (BmNPV) K1 strain. The 969 bp v-cath has an open reading frame of 323 amino acids. A putative cleavage site and catalytic sites were conserved in BmNPV-K1 v-cath. The predicted three-dimensional structure of BmNPV-K1 v-cath revealed that the overall fold of BmNPV-K1 v-cath is similar to that of other proteases of the papain family. The deduced amino acid sequence of BmNPV-K1 v-cath showed 98% and 97% protein sequence identity to BmNPV T3 strain and to Autographa californica nuclear polyhedrosis virus, respectively. The BmNPV-K1 v-cath differed at 4 amino acid positions from BmNPV T3. The v-cath gene in BmNPV-K1 genome is located on the EcoRV 6 kb and XhoI 9 kb fragments. Northern hybridization analysis of BmNPV K1 v-cath gene revealed that it is expressed late in infection.

• Molecules and Cells
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• v.38 no.9
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• pp.781-788
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• 2015

Mutations of MYO15A are generally known to cause severe to profound hearing loss throughout all frequencies. Here, we found two novel MYO15A mutations, c.3871C>T (p.L1291F) and c.5835T>G (p.Y1945X) in an affected individual carrying congenital profound sensorineural hearing loss (SNHL) through targeted resequencing of 134 known deafness genes. The variant, p.L1291F and p.Y1945X, resided in the myosin motor and IQ2 domains, respectively. The p.L1291F variant was predicted to affect the structure of the actin-binding site from three-dimensional protein modeling, thereby interfering with the correct interaction between actin and myosin. From the literature analysis, mutations in the N-terminal domain were more frequently associated with residual hearing at low frequencies than mutations in the other regions of this gene. Therefore we suggest a hypothetical genotype-phenotype correlation whereby MYO15A mutations that affect domains other than the N-terminal domain, lead to profound SNHL throughout all frequencies and mutations that affect the N-terminal domain, result in residual hearing at low frequencies. This genotype-phenotype correlation suggests that preservation of residual hearing during auditory rehabilitation like cochlear implantation should be intended for those who carry mutations in the N-terminal domain and that individuals with mutations elsewhere in MYO15A require early cochlear implantation to timely initiate speech development.

• Microbiology and Biotechnology Letters
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• v.47 no.1
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• pp.164-171
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• 2019

Radiation therapy has many side effects, such as digestive mucosal ulcers, without regard to its efficacy. The purpose of this study is to address an alternative method to replace the limitation of radiation therapy using radiomimetic microbial ribotoxins. In the evaluation of cancer therapy, we analyzed the formation of colorectal cancer (CRC) cell spheroids, which can take into account the heterogeneous cellular constitution, tumor stem cells, and the surrounding microenvironment. Ribotoxic stress interfered with the spheroid structure composed of relatively small clusters. Spheroids under ribotoxic stress were structurally sparse and their shrinkage was very slow. In the control group, the clusters of strongly aggregated cells were resistant to physical stress, but the ribotoxic stress-exposed spheroids were easily broken up by the physical stress. Moreover, the ribosome-insulted CRC cells slowly migrated to form clusters and the cell-cell junctional points in the ribosome-insulted spheroids were rarer than those in the control CRC spheroid. Moreover, levels of the cell-to-cell junctional protein E-cadherin were suppressed by ribotoxic stress in both allograft and xenograft spheroids. In conclusion, the radiomimetic microbial ribotoxins induced structural defects in CRC cell spheroids via retardation of migration and cell-cell junction in the formation of three-dimensional structures, and provides a basis for the mechanism of pharmacological radiomimetic anticancer actions as an alternate to radiotherapy against cancer.

• Journal of Life Science
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• v.28 no.3
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• pp.307-313
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• 2018

Alopecia cause psychological stress due to their effect on appearance. Thus, the global market size of the alopecia treatment products are growing quickly. Timosaponin A III is the well known active ingredient of Anemarrhenae Rhizoma. In this study, we investigated and compared the binding affinity of timosaponin A III with finasteride (5-beta reductase antagonist) and minoxidil (androgen receptor antagonist) on the target protein active site by in silico computational docking studies. The three dimensional crystallographic structure of 5-beta reductase (PDB ID : 3G1R) and androgen receptor (PDB ID: 4K7A) was obtained from PDB database. In silico computational autodocking analysis was performed using PyRx, Autodock Vina, Discovery Studio Version 4.5, and NX-QuickPharm option based on scoring functions. The timosaponin A III showed optimum binding affinity (docking energy) with 5-beta reductase as -12.20 kcal/mol as compared to the finasteride (-11.70 kcal/mol) and with androgen receptor as -9.00 kcal/mol as compared to the minoxidil (-7.40 kcal/mol). The centroid X, Y, Z grid position of the timosaponin A III on the 5-beta reductase was similar (overlap) to the finasteride, but the X, Y, Z centroid grid of the timosaponin A III on the androgen receptor was significantly far from the minoxidil centroid position. These results significantly indicated that timosaponin A III could be more potent antagonist to the 5-beta reductase and androgen receptor. Therefore, the extract of Anemarrhenae Rhizoma or timosaponin A III containing biomaterials can substitute the finasteride and minoxidil and can be applied to the alopecia protecting product and related industrial fields.