• 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.

• The Plant Pathology Journal
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• v.27 no.3
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• pp.285-290
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• 2011

Fusarium graminearum virus 2 (FgV2) infects Fusarium graminearum strain 98-8-60 and has at least five segments of double-stranded RNAs (dsRNAs), denoted as dsRNA-1 to dsRNA-5. In this study, the genome of FgV2 was sequenced and its phylogenetic relationship with other mycoviruses was analyzed. The lengths of FgV2 dsRNAs 1-5 ranged from 2414 to 3580 base pairs (bp). The 5' and 3' untranslated regions (UTRs) are highly conserved, and each dsRNA segment had 78-105 and 84-306 bp of 5' and 3' UTRs, respectively. Each dsRNA segment contained a single open reading frame (ORF). Computer analysis of dsRNA-1 revealed a putative open reading frame (ORF) that shows high sequence identity with an RNA-dependent RNA polymerase (RdRp) containing eight conserved motifs. dsRNAs 2-5 also each contain one putative ORF coding for products of unknown function. The sequences of FgV2 dsRNA-2 and dsRNA-3 have significant sequence identity with Magnaporthe oryzae chrysovirus 1 (MoCV1) dsRNA-3 and -4, respectively. When compared to other dsRNA mycoviruses in a phylogenetic analysis of the putative RdRp protein, FgV2 was found to form a distinct virus clade with Aspergillus mycovirus 1816 and MoCV1 in the family Chrysoviridae.

• Korean Institute of Interior Design Journal
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• v.21 no.2
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• pp.35-45
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• 2012

The development of digital media made the change of architectural paradigm from tectonic to the surface and pattern. This means the transition to the new kind of materiality and the resurrection of ornament. This study started as an aim to apply biological pattern to architectural design from the new perception of pattern. Architectural patterns in the early era appeared as ladders, steps, chains, trees, vortices. But since 21st century, we can find patterns in nature like atoms and molecular structures, fluid forms of dynamics and new geometrical pattern like fractal and first of all biological patterns like viruses and micro-organisms, Voronoi cells, DNA structure, rhizomes and various hybrids and permutations of these. Pattern became one of the most important elements and themes of contemporary architecture through the change of materiality and resurrection of ornament with the new perception of surface in architecture. One of the patterns that give new creative availability to the architectural design is biological pattern which is self-organized as an optimum form through interaction with environment. Biological patterns emerge mostly as self-replicating patterns through morphogenesis, certain geometrical patterns(in particular triangles, pentagons, hexagons and spirals). The architectural application methods of biological patterns are direct figural pattern of organism, circle pattern, polygon pattern, energy-material control pattern, differentiation pattern, parametric pattern, growth principle pattern, evolutionary ecologic pattern. These patterns can be utilized as practical architectural patterns through the use of computer programs as morphogenetic programs like L-system, MoSS program and genetic algorithm programs like Grasshoper, Generative Components with the help of computing technology like mapping and scripting.

• Asian-Australasian Journal of Animal Sciences
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• v.22 no.8
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• pp.1091-1101
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• 2009

In an attempt to understand the biochemical mechanism for the synthesis of the anabolic steroid, 19-nortestosterone, produced by prepubertal boar testes and its physiological role, normalized complementary DNA (cDNA) from boar testes was generated. DNA sequencing of 2,016 randomly selected clones yielded 794,116 base pairs of high quality nucleotide sequence. Computer-assisted assembly of the nucleotide sequence of each clone resulted in 423 contigs and 403 singletons including several genes for steroidogenic enzymes and molecules related to steroid metabolism. Analysis of gene expression pattern by use of the presently-fabricated cDNA microarray identified a number of genes that were differentially expressed during the postnatal development period in boar testes. Two genes of unknown function were identified to be highly expressed in the testis of 2-weeks-old neonatal boar. In addition, the sequencing of open reading frames of these genes revealed their homology with human alpha hemoglobin and Homo sapiens hypothetical LOC643669, transcript variant 1. Moreover, the transcripts of these genes were also detected in porcine muscle and adipocytes, in addition to Leydig cells of pigs.

• Journal of Microbiology and Biotechnology
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• v.17 no.7
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• pp.1079-1082
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• 2007

Chromosome microdissection and the reverse FISH technique is one of the most useful methods for the identification of structurally abnormal chromosomes. In particular, the laser microbeam microdissection (LMM) method allows rapid isolation of a target chromosome or a specific region of chromosomes without damage of genetic materials and contamination. Isolated chromosomes were directly amplified by the degenerate oligonucleotide-primed polymerase chain reaction (DOP-PCR), and then the FISH probes labeled with spectrum green- or spectrum red-dUTP were generated by nick-translation. Whole chromosome painting (WCP) probes were successfully generated from only 5 copies of the chromosome. With this method, we produced 24 WCP probes for each human chromosome. We also tried to characterize a marker chromosome, which seemed to be originated from chromosome 11 on conventional banding technique. The marker chromosomes were isolated by the LMM method and analyzed by reverse FISH. We elucidated that the marker chromosome was originated from the short arm of chromosome 5 ($5p11{\to}pter$). A fully automated and computer-controlled LMM method is a very simple laboratory procedure, and enables rapid and precise characterization of various chromosome abnormalities.

• Journal of the Korean Chemical Society
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• v.50 no.3
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• pp.196-202
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• 2006

The self diffusion distributions of viscoelastic molten polyurethanes were determined from the relationship between the relaxation spectra and the distribution of self diffusion. The relaxation spectra of ester, PCL and PCL dyed type molten polyurethanes were obtained by applying the experimental stress relaxation curves to the theoretical equation of the Ree-Eyring and Maxwell non-Newtonian model(REM model) from computer calculation. The experiments were carried out at various temperatures using the physica rheometer with the temperature controller. The self diffusion and hole distance of amorphous region of polyurethane samples were investigated by experiments of stress relaxation. The diffusion coefficients and hole volumes were calculated from rheological parameters and crystallite size in order to study the diffusion of flow segments in amorphous region. It was observed that the relaxation spectra and self diffusions of these polymer samples are directly related to the distribution of molecular weights, viscosities, hole volumes and activation energies of flow segments.

• Proceedings of the Korean Vacuum Society Conference
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• 1999.07a
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• pp.140-140
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• 1999

Ti/Ni multilayered films (MLF) are ideal for neutron optics particularly in neutron guides and focusing devices. This system also possesses the tendency of amorphization through a solid-state reaction (SSR). This behaviors are closely related to the electronic structures and both magneto-optical (MO) and optical properties of metals depend strongly on their electron energy structures. Mutual inter-diffusion of the Tin and Ni atoms in the MLF caused by a low temperature annealing should decrease the thickness of pure Ni, as well as change the chemical and atomic order in the reactive zone. The application of the MO spectroscopy to the study of SSR in the MLF allows us to obtain an additional information on the changes in the atomic and chemical orders in the interface region. The optical one has no restriction on the magnetic state of the constituent sublayers. Therefore, the changes in magnetic, MO and optical properties of the Ti/Ni MLF due to SSR can be expected. To the best of our knowledge, the MO and optical spectroscopies were not used for this purpose. SSR has been studied in the series of the Ti/Ni MLFs with bilayer periods of 0.65-22.2nm and constant ratio of the Ti to Ni sublayers thickness by using MO and optical spectroscopies as well as an x-ray diffraction. The experimental MO and optical spectra are compared with the computer-simulated spectra, assuming various interface models. The relative changes in the x-ray diffraction spectra and MO properties of the Ti/Ni MLF caused by annealing are bigger for the multilayers with "thick" sublayers, or the SSR with the formation of amorphous alloy takes place mainly in the Ti/Ni multilayers with "thick" sublayers, while in the nominal threshold thickness of the Ni-sublayer for the observation of the equatorial Kerr effect in the as-deposited and annealed Ti/Ni MLFs of about 3.0 and 4.5nm thick is explained by the formation of amorphous alloy during the deposition or the formation of the nonmagnetic alloyed regions between pure components as a result of the SSR. For the case of Ti/Ni MLF the MO approach is more sensitive for the determination of the thickness of the reacted zone, while x-ray diffraction is more useful for structural analyses.structural analyses.

• Journal of Korean Neurosurgical Society
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• v.59 no.5
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• pp.425-429
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• 2016

Objective : Rod-screw fixation systems are widely used for spinal instrumentation. Although many biomechanical studies on rod-screw systems have been carried out, but the effects of rod contouring on the construct strength is still not very well defined in the literature. This work examines the mechanical impact of straight, $20^{\circ}$ kyphotic, and $20^{\circ}$ lordotic rod contouring on rod-screw fixation systems, by forming a corpectomy model. Methods : The corpectomy groups were prepared using ultra-high molecular weight polyethylene samples. Non-destructive loads were applied during flexion/extension and torsion testing. Spine-loading conditions were simulated by load subjections of 100 N with a velocity of $5mm\;min^{-1}$, to ensure 8.4-Nm moment. For torsional loading, the corpectomy models were subjected to rotational displacement of $0.5^{\circ}\;s^{-1}$ to an end point of $5.0^{\circ}$, in a torsion testing machine. Results : Under both flexion and extension loading conditions the stiffness values for the lordotic rod-screw system were the highest. Under torsional loading conditions, the lordotic rod-screw system exhibited the highest torsional rigidity. Conclusion : We concluded that the lordotic rod-screw system was the most rigid among the systems tested and the risk of rod and screw failure is much higher in the kyphotic rod-screw systems. Further biomechanical studies should be attempted to compare between different rod kyphotic angles to minimize the kyphotic rod failure rate and to offer a more stable and rigid rod-screw construct models for surgical application in the kyphotic vertebrae.

• Journal of Microbiology
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• v.40 no.3
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• pp.211-218
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• 2002

A 4.8-kb DNA fragment encoding the P-450 type hydroxylase and ferredoxin genes was cloned from Pseudonocardia autotrophica IFO 12743 that can convert vitamin D$\_$3/ into its hydroxylated active forms. In order to isolate the P-450 gene cluster in this organism, we designed PCR primers on the basis of the regions of an oxygen binding site and a heme ligand pocket that are general characteristics of the P-450 hydroxylase. Sequencing analysis of the BamHI fragment revealed the presence of four complete and one incomplete ORFs, named PauA, PauB, PauC, and PauD, respectively. As a result of computer-based analyses, PauA and PauB have homology with enoyl-CoA hydratase from several organisms and the positive regulators belonging to the tetR family, respectively. PauC and PauD show similarity with SuaB/C proteins and ferredoxins, respectively, which are composed of P-450 monooxygenase systems for metabolizing two sulfonylurea herbicides in Streptomyces griseolus PauC shows the highest similarity with another CytP-450$\_$Sca2/ protein that is responsible for production of a specific HMG-CoA reductase inhibitor, pravastatin, in S. carbophilus. Cultures of Steptomyces lividans transformant, containing the P-450 gene cluster on the pWHM3 plasmid, was unable to convert vitamin D$\_$3/ to its hydroxylated forms.

• Applied Biological Chemistry
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• v.31 no.3
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• pp.274-283
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• 1988

Aqualysin I is an alkaline serine protease which is secretet into the culture medium by Thermus aquaticus YT-1, an extreme thermophile. Aqualysin I was purified, and its partial amino acid sequence was determined. The gene encoding aqualysin I was cloned into E. coli using synthetic oligodeoxyribonucleotides as hybridization probes. The nucleotide sequence of the cloned DNA was determined. The primary structure of aqualysin I, deduced from the nucleotide sequenc, agreed with the determid amino acid sequences, including the $NH_2-$ and COOH terminal sequence of the tryptides derived from aqualysin I. Aqualysin I comprised 281 amino acid residues and its molecular mass was determined to be 28350. On alignment of the whole amino acid sequence, aqualysin I showed high sequence homology with the subtilisin type serine protease, and 43% identity with proteinase K, 37-30% with subtilisins and 34% with thermitase. Extremely high sequence identity was observed in the regions containing the active-site residues, corresponding to Asp32, His64 and Ser221 of subtilisin BPN'. Aqualysin I contains two disulfide bonds, Cys67-Cys99 and Cys163-Cys194, and these disulfide bonds seem to contribute to the heat stability of the enzyme. The determined positions of the twe disulfide bonds of aqualysin I agreed with those predicted previously on the basis of computer graphics of the crystallographic data for subtilisin BPN'. Therefore, these findings sugests that the three-dimensional structure of aqualysin I is similar to that of subtilisin BPN' Aqualysin I is produced as a lage precursor, which contains $NH_2-$ and COOH- terminal portions besides the mature protease sequence.