• 식물조직배양학회지
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• 제26권1호
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• pp.41-47
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• 1999

토마토의 genomic DNA library로부터 분리한 tPALl, tPAL4유전자의 염기서열을 분석하여 tPAL5 유전자와 비교 분석한 결과는 다음과 같다. tPAL5 유전자는 722개의 아미노산과 710 bp의 intron을 가지고 있으나 tPALl은 intron을 가지고 있지 않으며 또한 tPAL5 유전자와 비교하여 249개의 짧은 polypeptide를 가지고 있었다. tPAL4유전자인 경우 357개의 아미노산과 305bp의 intron을 가지고 있었다. tPAL 효소간의 아미노산 homology는 tPAL1유전자와 tPAL4 유전자간은 87.2%, tPALl과 tPAL5는 85.3%, tPAL4 와 tPAL5 는 91.4%의 homology를 보였다. 또한, tPALl, tPAL4 유전자는 정상적인 polypeptide를 가지는 tPAL5유전자와 비교하여 비정상적인 stop codon을 가진 짧은 polypeptide로 구성되어 있었다. 다양한 식물 종으로부터 분리된 PAL유전자의 염기서열을 비교한 결과 토마토 (Lycopersicon esculentum), 감자 (Solanum tuberosum), 고구마 (Ipomoea batatas)간의 유연관계과 높았으며, parsley (Petroselinum crispum), bean (Phaseolus vulgaris), pea (Pisum sativum), alfalfa (Medicago sativa) 등이 각각 서로간에 유연관계가 높았다. 또한, 토마토에서 분리한 family내에서 tPAL4와 tPAL5 유전자는 homology가 매우 높았고 (93.0%), tPAL1와 tPAL4유전자 사이는 다소 낮았으며 (84.4%), 특히 tPAL4는 감자의 PAL 유전자와 매우 높았다 (90.6%).

• 대한기계학회논문집A
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• 제20권3호
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• pp.872-881
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• 1996

The concept of homology design has been devised for the application to large telescope structure by S.v.Hoerner. It is defined that the deformation of a structure shall be called homologous, if a given geometrical relation holds, for a given number of structural points, before, during, and after the deformation. Recently, the need of homology design in the structural design has been increase due to the required precision in the structure. Some researchers have utilized the theory on the structural design with finite element method in the late 1980s In the present investigation, a simple method using geometrical equality constraints is suggested to gain homologous deformation. The previous method is improved in that the decomposition of FEM eqation, which is very expensive, is not necessary. The basic formulations of the homology design with the optimization concept are described and several practical examples are solved to verify the usefulness and validity. Especially, a back-up structure of a satellite antenna is designed by the suggested method. The results are compared with those of existing researches.

• BMB Reports
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• 제39권5호
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• pp.578-585
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• 2006

The cDNA of a firefly luciferase from lantern mRNA of Lampyroidea maculata has been cloned, sequenced and functionally expressed. The cDNA has an open reading frame of 1647 bp and codes for a 548-residue-long polypeptide. Noteworthy, sequence comparison as well as homology modeling showed the highest degree of similarity with H. unmunsana and L. mingrelica luciferases, suggesting a close phylogenetic relationship despite the geographical distance separation. The deduced amino acid sequence of the luciferase gene of firefly L. maculata showed 93% identity to H. unmunsana. Superposition of the three-dimensional model of L. maculata luciferase (generated by homology modeling) and three dimensional structure of Photinus pyralis luciferase revealed that the spatial arrangements of Luciferin and ATP-binding residues are very similar. Putative signature of AMP-binding domain among the various firefly species and Lampyroidea maculata was compared and a striking similarity was found. Different motifs and sites have been identified in Lampyroidea maculata by sequence analysis. Expression and purification of luciferase from Lampyroidea maculata was carried out using Ni-NTA Sepharose. Bioluminescence emission spectrum was similar to Photinus pyralis luciferase.

• Asian-Australasian Journal of Animal Sciences
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• 제16권12호
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• pp.1816-1821
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• 2003

Reliable PCR based identification of lactobacilli has been described utilizing the sequence of 16S-23S rRNA intergenic spacer region. Those sequence comparisons showed a high degree of difference in homology among the strains of L. rhamnosus, L. casei, L. acidophilus and L. helveticus whose 16S-23S rRNA intergenic small SR's sizes were 222 bp, 222 bp, 206 bp and 216 bp respectively. The sequence of 16S-23S rRNA intergenic spacer region of L. rhamnosus ATCC 53103 revealed the close relatedness to those of L. casei strains by the homology ranges from 95.4% to 97.2%. 16S-23S rRNA intergenic spacer region nucleotide sequence of L. acidophilus showed some distant relatedness with L. rhamnosus ATCC 53103 with the homology ranges from 40.3% to 41.8% and that with L. helveticus was shown to be 30% of homology, which exists at the most distant phylogenetic relatedness. The identification of species and strain of lactobacilli was possible on the basis of these results. The common sequences among the 17 strains were CTAAGGAA located in the initiating position of the DNA and some discrepancies were found between the same strains based on these results.

• Bulletin of the Korean Chemical Society
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• 제33권6호
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• pp.1885-1889
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• 2012

Among 23 cytochrome P450s, CYP125A4 was proposed as a putative monooxygenase based on the high level of amino acid sequence homology (54% identity and 75% similarity) with the well characterized C27-steroid $Mycobacterium$ $tuberculosis$ CYP125A1. Utilizing MTBCYP125A1 as a template, homology modeling of SPCYP125A4 was conducted by Accelrys Discovery Studio 3.1 software. The modeled SPCYP125A4 structure with lowest energy value was subsequently assessed for its stereochemical quality and side-chain environment. The final model was generated by showing its active site through the molecular dynamics. The docking of steroids showed broad specificity of SPCYP125A4 with different orientation of ligand within active site facing the heme. One poses of C27-steroid with C26 facing the heme with distance of 3.734 ${\AA}$ from the Fe were predominant.

• Bulletin of the Korean Chemical Society
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• 제32권6호
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• pp.2008-2014
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• 2011

Serotonin or 5-hydroxytryptamine subtype 2C ($5-HT_{2C}$) receptor belongs to class A amine subfamily of G-protein-coupled receptor (GPCR) super family and its ligands has therapeutic promise as anti-depressant and -obesity agents. So far, bovine rhodopsin from class A opsin subfamily was the mostly used X-ray crystal template to model this receptor. Here, we explained homology model using beta 2 adrenergic receptor (${\beta}$2AR), the model was energetically minimized and validated by flexible ligand docking with known agonists and antagonists. In the active site Asp134, Ser138 of transmembrane 3 (TM3), Arg195 of extracellular loop 2 (ECL2) and Tyr358 of TM7 were found as important residues to interact with agonists. In addition to these, V208 of ECL2 and N351 of TM7 was found to interact with antagonists. Several conserved residues including Trp324, Phe327 and Phe328 were also found to contribute hydrophobic interaction. The predicted ligand binding mode is in good agreement with published mutagenesis and homology model data. This new template derived homology model can be useful for further virtual screening based lead identification.

• 대한수의학회지
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• 제38권1호
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• pp.53-63
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• 1998

Total of 1085 swine sera (1996-1997) from nation-wide were tested for the presence of antibodies to influenza A virus. Fifty nine percent of the tested sera showed seropositive by HI test. Positive sera consisted of 24--- of H3, 15--- of H1, and 20--- of the sample had both antibodies, respectively. Sera collected from various region represented 7~27--- seropositivity to H1N1, 15~25--- to H3N2, respectively. Swine influenza field isolate from nasal swab was characterized antigenically and genetically to elucidate its relatedness with other known strains of influenza A virus. The study was focused on the HA gene which is related to pathogenecity and antigenic variability of the influenza virus. By RT-PCR using influenza A/H1N1 specific primers, influenza virus H1N1 specific DNA fragment was amplified from A/Swine/Iowa/15/30(H1N1), US field isolate but not in H3N2 strain. PCR products were sequenced by dideoxy chain termination method to determine nucleotide homology with other strains of influenza A virus. The US field isolate and A/Swine/Indiana/1726/88 strain had 97--- of nucleotide homology and 98--- of amino acid homology. Based on the results obtained from this experiment, the field isolate was genetically related to A/Swine/Indiana/1726/88 and had higher homology with A/Swine/Indiana/1726/88 than with classical swine influenza virus, A/Swine/Iowa/15/30. The field isolate had no amino acid changes at the antigenic site compare to that of the A/Swine/Indiana/1726/88. The proteolytic enzyme cleavage site between HA1 and HA2 had no alteration and the amino acid arginine was intact. There is no evidence has been found that the field isolate has genetic shift or genetic drift which might altered antigenic determinant.

• 생명과학회지
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• 제19권11호
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• pp.1522-1528
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• 2009

알긴산을 분해하기 위하여 갈조류로부터 분해활성이 있는 해양미생물을 분리하였다. 분리된 균주의 16S ribosomal DNA를 분석한 결과 이전에 보고했던 ALG-5 균주와 비슷한 Streptomyces sp.에 속하는 것으로 나타났다. 상동성이 있는 염기서열로 고안한 특이적인 primer로 PCR을 행함로서 Streptomyces sp. M3의 새로운 alginate lyase 유전자를 클로닝하였다. M3 alginate lyase의 예상 아미노산 서열에는 N-terminal 영역에 YXRSELREM 서열과 C-terimnal 영역에 YFKAGXYXQ 서열이 보존되어 있었다. M3 alginate lyase 단백질의 homology model은 Corynebacterium sp. ALY-1으로부터 얻은 단백질인 alyPG와 같이 $\beta$-jelly roll fold를 main domain으로 가지고 있음이 나타났다. M3 alginate lyase 유전자를 가지는 재조합 E. coli의 세포균질액은 polymannuronate block보다는 polyguluronate block에 대하여 높은 분해력을 가지고 있었다. 아미노산 서열 다중정열 및 homology modeling으로부터 얻은 결과는 M3 alginate lyase가 Family PL-7으로 분류될 수 있음을 말해 준다.

• 한국멀티미디어학회논문지
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• 제19권2호
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• pp.146-154
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• 2016

This paper presents methods to analyze the topological structures of the spaces composed of patches extracted from waveform signals, which can be applied to the classification of signals. Commute time embedding is performed to transform the patch sets into the corresponding geometries, which has the properties that the embedding geometries of periodic or quasi-periodic waveforms are represented as closed curves on the low dimensional Euclidean space, while those of aperiodic signals have the shape of open curves. Persistent homology is employed to determine the topological invariants of the simplicial complexes constructed by randomly sampling the commute time embedding of the waveforms, which can be used to discriminate between the groups of waveforms topologically.