• Proceedings of the Computational Structural Engineering Institute Conference
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• 2002.04a
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• pp.319-326
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• 2002

A p-version finite element model based on degenerate shell element is proposed for the analysis of orthotropic laminated plates. In the nonlinear formulation of the model, the total Lagrangian formulation is adopted with large deflection and moderate rotation being accounted for in the sense of von Karman hypothesis. The material model Is based on the Huber-Mises yield criterion and Prandtl-Reuss flow rule in accordance with the theory of strain hardening yield function, which is generalized for anisotropic materials by introducing the parameters of anisotropy. The model is also based on extension of equivalent-single layer laminate theory(ESL theory) with shear deformation, leading to continuous shear strain at the interface of two layers. The Integrals of Legendre Polynomials we used for shape functions with p-level varying from 1 to 10. Gauss-Lobatto numerical quadrature is used to calculate the stresses at the nodal points instead of Gauss points. The validity of the proposed p-version finite element model is demonstrated through several comparative points of view in terms of ultimate load, convergence characteristics, nonlinear effect, and shape of plastic zone

• Progress in Medical Physics
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• v.19 no.3
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• pp.157-163
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• 2008

Retinal prosthesis is regarded as the most feasible method for the blind caused by retinal diseases such as retinitis pigmentosa or age-related macular degeneration. One of the prerequisites for the success of retinal prosthesis is the optimization of the electrical stimuli applied through the prosthesis. Since electrical characteristics of degenerate retina are expected to differ from those of normal retina, we investigated differences of the retinal waveforms in normal and degenerate retina to provide a guideline for the optimization of electrical stimulation for the upcoming prosthesis. After isolation of retina, retinal patch was attached with the ganglion cell side facing the surface of microelectrode arrays (MEA). $8{\times}8$ grid layout MEA (electrode diameter: $30{\mu}m$, electrode spacing: $200{\mu}m$, and impedance: 50 $k{\Omega}$ at 1 kHz) was used to record in-vitro retinal ganglion cell activity. In normal mice (C57BL/6J strain) of postnatal day 28, only short duration (<2 ms) retinal spikes were recorded. In rd/rd mice (C3H/HeJ strain), besides normal spikes, waveform with longer duration (~100 ms), the slow wave component was recorded. We attempted to understand the mechanism of this slow wave component in degenerate retina using various synaptic blockers. We suggest that stronger glutamatergic input from bipolar cell to the ganglion cell in rd/rd mouse than normal mouse contributes the most to this slow wave component. Out of many degenerative changes, we favor elimination of the inhibitory horizontal input to bipolar cells as a main contributor for a relatively stronger input from bipolar cell to ganglion cell in rd/rd mouse.

• Journal of the Computational Structural Engineering Institute of Korea
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• v.15 no.3
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• pp.491-499
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• 2002

A p-version finite element model based on degenerate shell element is proposed tot the analysis of orthotropic laminated plates. In the nonlinear formulation of the model, the total Lagrangian formulation is adopted with large deflection and moderate rotation being accounted tot in the sense of yon Karman hypothesis. The material model is based on the Huber-Mises yield criterion and Prandtl-Reuss flow rule in accordance with the theory of strain hardening yield function, which is generalized lot anisotropic materials by introducing the parameters of anisotropy. The model is also based on extension of equivalent-single layer laminate theory(ESL theory) with shear deformation, leading to continuous shear strain at the interface of two layers. The integrals of Legendre polynomials are used for shape functions with p-level varying from 1 to 10. Gauss-Lobatto numerical quadrature is used to calculate the stresses at the nodal points instead of Gauss points. The validity of the proposed P-version finite element model is demonstrated through several comparative points of iew in terms of ultimate load, convergence characteristics, nonlinear effect, and shape of plastic tone.

• Journal of Microbiology and Biotechnology
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• v.12 no.5
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• pp.819-825
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• 2002

Methanol dehydrogenase (MDH) is a key enzyme in the process of methanol oxidation in methylotrophic bacteria. However, information on MDH genes from genus Methylobacillus is limited. In this study, a 6.5-kb HindIII DNA fragment of Methylobacillus sp. SK-5 chromosomal DNA was isolated from the genomic library of the strain by using a degenerate oligonucleotide probe that was designed based on JV-terminal amino acid sequence of the MDH $\alpha$ subunit purified from the strain. Molecular analysis of the fragment revealed four tightly clustered genes (mxaFJGI) involved in the methanol oxidation. The first and fourth genes were very similar to mxaF (77% identity for nucleotides an 78% identity for amino acids) and mxaF (67% Identity for nucleotides and 68% Identity for amino acids) genes, respectively, from Methylovorus sp. SSI. Genes mxaF and mxaI encode $\alpha$ and $\beta$ subunits of MDH, respectively. The two subunits were identified from purified MDH from Methylobacillus sp. SK-5. A dendrogram constructed by comparison of amino acid sequences of MDH u subunits suggests that MxaF from Methylobacillus sp. SK-5 belongs to a subfamily cluster of MDH u subunits from $\beta$-subgroup Proteobacteria. The subfamily cluster is separated from the other subfamily that consists of $\beta$- and $\gamma$-subgroup Proteobacteria. This study provided information on mn genes from a methylotrophic bacterium in $\beta$-subgroup Proteobacteria, which would aid to better develop a gene probe to detect one-carbon metabolizing bacteria.

• 한국생물공학회:학술대회논문집
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• 2005.04a
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• pp.420-422
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• 2005

TMC (Tautomycetin) is a liner polyketide immunosuppressive antifungal compound produced by Streptomyces spp. Inhibition of T cell proliferation with TMC was observed highly efficient at 100-fold lower than those needed to achieve maximal inhibition with cyclosporin A. To elucidate the biosynthetic pathway of TMC, a genomic DNA library was constructed using a E. coil-Streptomyces shuttle cosmid vector, pOJ446. The DNA libraries were screened by colony blot hybridization using several polyketide ${\beta}-ketosynthase$ (KS) probes amplified from TMC-producing Streptomyces genomic DNA using polymerase chain reaction (PCR), of which the degenerate primers were designed based on the highly conserved sequences present in KS domains of various type I polyketide synthase genes in Streptomyces species. This library construction and screening approach led to the isolation of several positive cosmid clones representing type I polyketide biosynthetic gene clusters. In addition, a Streptomyces regulatory gene called afsR2 (a global regulatory gene stimulating antibiotic production in both S. coelicolor and S. lividans) was successfully integrated into the TMC-producing Streptomyces chromosome via E. coil-Streptomyces heterologous conjugation mehtod. The more detailed results of production improvement and genetic characterization of TMC-producing Streptomyces spp. will be discussed.

• Journal of the Korean Society for Precision Engineering
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• v.20 no.11
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• pp.150-157
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• 2003

In this paper, the large deformation of hollow silicon rubber gasket is treated. The frictional contact occurs between groove and the outer part of hollow gasket, and the frictional self-contact exists in the inner parts of hollow gasket. The silicon rubber has the nonlinear elastic behavior and its material property is approximately incompressible. Hence, the stress analysis requires an existence of a strain energy function, which is usually defined in terms of invariants or stretch ratio such as generalized Mooney-Rivlin and Ogden model. Considering large compressive deformation and friction, Mooney-Rivlin 3rd model and Coulomb's friction model are assumed. The numerical analysis is obtained by the commercial finite element program MARC. But, due to large deformation, the elements degenerate in the inner parts of hollow gasket. This means that the analysis of subsequent increments is carried out with a very poor mesh. In order to continue the analysis with a sufficient accuracy, it is necessary to use new finite element modeling by remesh. Experiments are also performed to show the validity of present method. As a conclusion, numerical results by this research have good agreements with experiments.

• Journal of Microbiology and Biotechnology
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• v.22 no.6
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• pp.742-753
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• 2012

Copper-containing compounds are introduced into the environment through agricultural chemicals, mining, and metal industries and cause severe detrimental effects on ecosystems. Certain microorganisms exposed to these stressors exhibit molecular mechanisms to maintain intracellular copper homeostasis and avoid toxicity. We have previously reported that the soil bacterial isolate Achromobacter sp. AO22 is multi-heavy metal tolerant and exhibits a mer operon associated with a Tn21 type transposon. The present study reports that AO22 also hosts a unique cop locus encoding copper homeostasis determinants. The putative cop genes were amplified from the strain AO22 using degenerate primers based on reported cop and pco sequences, and a constructed 10,552 base pair contig (GenBank Accession No. GU929214). BLAST analyses of the sequence revealed a unique cop locus of 10 complete open reading frames, designated copSRABGOFCDK, with unusual separation of copCD from copAB. The promoter areas exhibit two putative cop boxes, and copRS appear to be transcribed divergently from other genes. The putative protein CopA may be a copper oxidase involved in export to the periplasm, CopB is likely extracytoplasmic, CopC may be periplasmic, CopD is cytoplasmic/inner membrane, CopF is a P-type ATPase, and CopG, CopO, and CopK are likely copper chaperones. CopA, B, C, and D exhibit several potential copper ligands and CopS and CopR exhibit features of two-component regulatory systems. Sequences flanking indicate the AO22 cop locus may be present within a genomic island. Achromobacter sp. strain AO22 is thus an ideal candidate for understanding copper homeostasis mechanisms and exploiting them for copper biosensor or biosorption systems.

• Parasites, Hosts and Diseases
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• v.40 no.1
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• pp.17-24
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• 2002

We have cloned a cDNA encoding a cysteine proteinase of the Acanthamoeba healui OC-3A strain isolated from the brain of a granulomatous amoebic encephalitis patient. A DNA probe for an A. healui cDNA library screening was amplified by PCR using degenerate oligonucleotide primers designed on the basis of conserved amino acids franking the active sites of cysteine and asparagine residues that are conserved in the eukaryotic cysteine proteinases. Cysteine proteinase gene of A. healui (AhCPI) was composed of 330 amino acids with signal sequence, a proposed pro-domain and a predicted active site made up of the catalytic residues, $Cys^{25},{\;}His^{159},{\;}and{\;}Asn^{175}$. Deduced amino acid sequence analysis indicates that AhCPI belong to ERFNIN subfamily of C 1 peptidases. By Northern blot analysis. no direct correlation was observed between AhCPI mRNA expression and virulence of Acanthamoeba, but the gene was expressed at higher level in amoebae isolated from soil than amoeba from clinical samples. These findings raise the possibility that AhCPI protein may play a role in protein metabolism and digestion of phagocytosed bacteria or host tissue debris rather than in invasion of amoebae into host tissue.

• Journal of Microbiology and Biotechnology
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• v.18 no.1
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• pp.160-166
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• 2008

A DNA fragment containing 2,079 base pairs from Bacillus circulans CGMCC 1416 was cloned using degenerate PCR and inverse PCR. An open reading frame containing 981 bp was identified that encoding 326 amino acids residues, including a putative signal peptide of 31 residues. The deduced amino acid sequence showed the highest identity (68.1%) with $endo-{\beta}-1,4-D-mannanase$ from Bacillus circulans strain K-1 of the glycoside hydrolase family 5 (GH5). The sequence encoding the mature protein was cloned into the pET-22b(+) vector and expressed in Escherichia coli as a recombinant fusion protein containing an N-terminal hexahistidine sequence. The fusion protein was purified by $Ni^{2+}$ affinity chromatography and its hexahistidine tag cleaved to yield a 31-kDa ${\beta}$-mannanase having a specific activity of 481.55U/mg. The optimal activity of the purified protein, MANB48, was at $58^{\circ}C$ and pH 7.6. The hydrolysis product on substrate locust bean gum included a monosaccharide and mainly oligosaccharides. The recombinant MANB48 may be of potential use in the feed industry.

• Journal of Microbiology and Biotechnology
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• v.20 no.10
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• pp.1440-1445
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• 2010

Rhodococcus sp. JDC-11, capable of utilizing di-n-butyl phthalate (DBP) as the sole source of carbon and energy, was isolated from sewage sludge and confirmed mainly based on 16S rRNA gene sequence analysis. The optimum pH, temperature, and agitation rate for DBP degradation by Rhodococcus sp. JDC-11 were 8.0, $30^{\circ}C$, and 175 rpm, respectively. In addition, low concentrations of glucose were found to inhibit the degradation of DBP, whereas high concentrations of glucose increased its degradation. Meanwhile, a substrate utilization test showed that JDC-11 was also able to utilize other phthalates. The major metabolites of DBP degradation were identified as monobutyl phthalate and phthalic acid by gas chromatography-mass spectrometry, allowing speculation on the tentative metabolic pathway of DBP degradation by Rhodococcus sp. JDC-11. Using a set of new degenerate primers, a partial sequence of the 3,4-phthalate dioxygenase gene was obtained from JDC-11. Moreover, a sequence analysis revealed that the phthalate dioxygenase gene of JDC-11 was highly homologous to the large subunit of the phthalate dioxygenase from Rhodococcus coprophilus strain G9.