• The Journal of the Korea Contents Association
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• v.18 no.4
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• pp.99-113
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• 2018

Recently, global warming has widened the habitat of mosquitoes and infection chances for mosquito-borne diseases are increasing. Flavivirus is a typical mosquito-borne virus. Flaviviruses with a relatively high frequency of infection in Asian countries include Zika, Dengue, and Japanese encephalitis viruses. Although distinctive diagnosis of flaviviruses is required because the symptoms and therapeutic method differ, there is no diagnostic method that can distinguish them accurately yet. In this study, we propose distinctive diagnosis method of flaviviruses using informations and analysis tools constructed in bioinformatic databases. The envelope protein and non-structural protein 1 which are useful protein for the immuno-diagnostics of three flaviviruses were selected. Their homology was analyzed by multiple sequence alignments and epitope candidates consisting of 10-15 amino acids were selected. Finally two epitopes were suggested to be most useful by immunogenicity analysis and 3D structure prediction. These approaches and results are expected to be great value in the distinctive diagnosis of three flaviviruses with a high frequency of infection in Asian countries.

• Proceedings of the Korea Information Processing Society Conference
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• 2003.11a
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• pp.389-392
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• 2003

인터넷상의 생물학 자원들을 이용하는 에이전트 시스템들에는 몇 가지 특징들이 있는데, 그중 하나가 바로 사용자 에이전트와 공개 데이터베이스들을 대신하는 에이전트들간의 자원 이용과정에서 발생하는 정보를 효율적으로 중계하고 조정하는 역할을 하는 기능이 존재해야 한다는 것이다. 공개 데이터베이스 자원들을 이용하는 경우 서로 다른 데이터 양식과 용어 체계, 제공하는 정보의 양과 정보를 제공하는데 걸리는 시간 등의 차이점이 존재하며, 또한 하나의 UI 에이전트로부터 복수 개의 질의를 수행하는 경우나 복수 개의 UI 에이전트들로부터 복수 개의 질의가 이루어지는 경우, 다양한 형태와 제공 정보로 인해 발생하는 자원들의 특성이 존재하게 된다. 이를 해결하기 위해서는 자원들의 다양성에 대한 고려, 메시지 트랜잭션의 관리와 더불어 다양한 플랫폼들에서 운용이 가능한 메시지 형식을 띠고 있어야 한다. 본 논문에서는 현재 개발중인 단백질 구조예측 연구를 지원하는 APSS 시스템 내에서의 사용자 에이전트와 여러 분석 및 자원 에이전트들 간의 효율적인 메시지 중재 및 조정기능을 갖는 CODY 에이전트를 설계하였고 이에 관하여 기술하고자 한다.

• Natural Product Sciences
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• v.25 no.3
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• pp.215-221
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• 2019

Inflammation is the crucial biological process of immune system which acts as body's defense and protective response against the injuries or infection. However, the systemic inflammation devotes the adverse effects such as multiple inflammation associated diseases. One of the best ways to treat this entity is by blocking the tumor necrosis factor alpha ($TNF-{\alpha}$) and TNF-related apoptosis-inducing ligand (TRAIL) to avoid the proinflammation cytokines production. Thus, this study aims to evaluate the potency of Sambucus bioactive compounds as anti-inflammation through in silico approach. In order to assess that, molecular docking was performed to evaluate the interaction properties between the $TNF-{\alpha}$ or TRAIL with the ligands. The 2D structure of ligands were retrieved online via PubChem and the 3D protein modeling was done by using SWISS Model. The prediction results of the study showed that caffeic acid (-6.4 kcal/mol) and homovanillic acid (-6.6 kcal/mol) have the greatest binding affinity against the $TNF-{\alpha}$ and TRAIL respectively. This evidence suggests that caffeic acid and homovanillic acid may potent as anti-inflammatory agent against the inflammation associated diseases. Finally, this study needs further examination and evaluation to validate the potency of Sambucus bioactive compounds.

• Korean Journal of Microbiology
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• v.42 no.4
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• pp.294-298
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• 2006

An immunoaffinity chromatography for the specific binding of Streptomyces somaliensis phospholipase D (PLD) that is considered as an industrially potential enzyme was developed. By using the protein structure prediction programs and the X-ray crystal structure of a Streptomyces PLD, 5 different epitopes with high antigenicity that are predicted to locate on the surface of the S. somaliensis PLD were selected and then synthesized for the preparation of antipeptide antibodies. Each purified rabbit IgG was coupled with NHS-activated Sepharose to prepare the immunoaffinity resins. After one-step purification of the culture concentrate on the antipeptide IgG-coupled Sepharose column, SDS-PAGE and the Western blot analysis of the purified samples showed that purification of PLD on the affinity columns was satisfactory, indicating that the peptide design using the structural information of Streptomyces PLDs was rational. However, the purified PLD in the solution aggregated rapidly, which resulted in poor specific activity and low purification yield.

• Asian-Australasian Journal of Animal Sciences
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• v.28 no.6
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• pp.870-875
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• 2015

The purpose of this study was to investigate the alternative splicing in equine cordon-bleu WH2 repeat protein-like 1 (COBLL1) gene that was identified in horse muscle and blood leukocytes, and to predict functional consequences of alternative splicing by bioinformatics analysis. In a previous study, RNA-seq analysis predicted the presence of alternative spliced isoforms of equine COBLL1, namely COBLL1a as a long form and COBLL1b as a short form. In this study, we validated two isoforms of COBLL1 transcripts in horse tissues by the real-time polymerase chain reaction, and cloned them for Sanger sequencing. The sequencing results showed that the alternative splicing occurs at exon 9. Prediction of protein structure of these isoforms revealed three putative phosphorylation sites at the amino acid sequences encoded in exon 9, which is deleted in COBLL1b. In expression analysis, it was found that COBLL1b was expressed ubiquitously and equivalently in all the analyzed tissues, whereas COBLL1a showed strong expression in kidney, spinal cord and lung, moderate expression in heart and skeletal muscle, and low expression in thyroid and colon. In muscle, both COBLL1a and COBLL1b expression decreased after exercise. It is assumed that the regulation of COBLL1 expression may be important for regulating glucose level or switching of energy source, possibly through an insulin signaling pathway, in muscle after exercise. Further study is warranted to reveal the functional importance of COBLL1 on athletic performance in race horses.

• Asian-Australasian Journal of Animal Sciences
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• v.30 no.3
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• pp.328-337
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• 2017

Objective: An experiment was conducted to determine the relationship between the KAP11.1 and the regulation wool fineness. Methods: In previous work, we constructed a skin cDNA library and isolated a full-length cDNA clone termed KAP11.1. On this basis, we conducted a series of bioinformatics analysis. Tissue distribution of KAP11.1 mRNA was performed using semi-quantitative reverse transcription polymerase chain reaction (RT-PCR) analysis. The expression of KAP11.1 mRNA in primary and secondary hair follicles was performed using real-time PCR (real-time polymerase chain reaction) analysis. The expression location of KAP11.1 mRNA in primary and secondary hair follicles was performed using in situ hybridization. Results: Bioinformatics analysis showed that KAP11.1 gene encodes a putative 158 amino acid protein that exhibited a high content of cysteine, serine, threonine, and valine and has a pubertal mammary gland) structural domain. Secondary structure prediction revealed a high proportion of random coils (76.73%). Semi-quantitative RT-PCR showed that KAP11.1 gene was expressed in heart, skin, and liver, but not expressed in spleen, lung and kidney. Real time PCR results showed that the expression of KAP11.1 has a higher expression in catagen than in anagen in the primary hair follicles. However, in the secondary hair follicles, KAP11.1 has a significantly higher expression in anagen than in catagen. Moreover, KAP11.1 gene has a strong expression in inner root sheath, hair matrix, and a lower expression in hair bulb. Conclusion: We conclude that KAP11.1 gene may play an important role in regulating the fiber diameter.

• Korean Chemical Engineering Research
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• v.55 no.1
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• pp.27-33
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• 2017

The determination of disulfide bonds is important for comprehensive understanding of the chemical structure of protein. So far, many strategies for the disulfide bond analysis have been suggested in terms of speed and sensitivity. However, most of these strategies have not considered free thiol residues in the target protein in the process of determining the disulfide bond. We suggested the strategy which was composed of four steps for the identification of disulfide bonds; the first step was the prediction of possible disulfide bonds, the second step was the determination of free cysteine residues, the third step was the analysis of disulfide bond using a high-resolution mass spectrometry, and the final step was the determination of disulfide bonds based on the comprehensive verification. In this study, we performed the characterization of disulfide bonds for the recombinant protein (HRPE1), where 1 and 5 inter- and intra-chain disulfide bonds were identified, respectively.

• Journal of Life Science
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• v.31 no.1
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• pp.83-89
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• 2021

Uu-ilys, an i-type lysozyme from spoon worm (Urechis unicinctus), is an innate immune factor that plays an important role in the defense against pathogens. It also possesses non-enzymatic antibacterial activity. Thus, there is a possibility to develop an antimicrobial model peptide from Uu-ilys. In this study, we report the design, production, and antibacterial activity of an Uu-ilys analog that exhibits antibacterial activity. The Uu-ilys structure was fragmented according to its secondary structures to predict the regions with antimicrobial activity using antimicrobial peptide (AMP) prediction tools from different AMP databases. A peptide containing the C-terminal fragment was predicted to exert antimicrobial activity. The chosen fragment was designated as an Uu-ilys analog containing the C-terminal fragment, Uu-ilys-CF. To examine the possibility of developing an AMP using the sequence of Uu-ilys-CF, recombinant fusion protein (TrxA-Uu-ilys-CF) was produced in an expression system that was heterologous. The produced fusion protein was cleaved after methionine leaving Uu-ilys-CF free from the fusion protein. This was then isolated through high performance liquid chromatography and reverse phase column, CapCell-Pak C18. The antibacterial activity of Uu-ilys-CF against different microbial strains (four gram-positive, six gram-negative, and one fungal strain) were assessed through the ultrasensitive radial diffusion assay (URDA). Among the bacterial strains tested, Salmonella enterica was the most susceptible. While the fungal strain tested was not susceptible to Uu-ilys-CF, broad spectrum antibacterial activity was observed.

• Journal of Plant Biotechnology
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• v.35 no.4
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• pp.317-327
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• 2008

Phytocystatins, which are inhibitors of plant cysteine peptidases, are involved in the regulation of protein turnover and in the defense against insect pests and pathogens. Extensive searches in the Brassica rapa genome allowed the prediction of at least eight different phytocystatin genes on seven chromosomes in the B. rapa genome. Structure comparisons based on alignments of the all BrCYS ($\underline{B}$. $\underline{r}apa$ $phyto{\underline{cys}}tatin$) proteins using the CLUSTALW program revealed conservation of the three consensus motifs known to interact with the active site of cysteine peptidases. According to the phylogenetic analysis based on the deduced amino acid sequences, the eight BrCYS proteins were divided into several clusters related to the orthologous phytocystatin. The predicted three-dimensional structure models of the eight BrCYS proteins demonstrate that all of these proteins are similar to the reported crystal structure of oryzacystatin-I (OC-I). Digital northern and RT-PCR analyses indicated that the eight BrCYS genes exhibit different expression patterns in B. rapa tissues and respond differently to abiotic stimuli. The differences in gene structure and expression between the eight BrCYS genes suggest that these proteins may play diverse physiological roles in B. rapa and may interact with cysteine peptidases through different mechanisms.

• The Journal of the Korea Contents Association
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• v.10 no.6
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• pp.166-174
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• 2010

Based on the theoretical results that multi-layer feedforward neural networks with enough hidden nodes are universal approximators, we usually use three-layer MLP's(multi-layer perceptrons) consisted of input, hidden, and output layers for many application problems. However, this conventional three-layer architecture of MLP shows poor generalization performance in some applications, which are complex with various features in an input vector. For the performance improvement, this paper proposes a hierarchical architecture of MLP especially when each part of inputs has a special information. That is, one input vector is divided into sub-vectors and each sub-vector is presented to a separate MLP. These lower-level MLPs are connected to a higher-level MLP, which has a role to do a final decision. The proposed method is verified through the simulation of protein disorder prediction problem.