• Journal of Microbiology and Biotechnology
• /
• 제12권1호
• /
• pp.130-136
• /
• 2002

The internal transcribed spacer (ITS) region in the genus Tricholoma was analyzed, including for its primary nucleotide sequence and secondary structural characterization. The secondary structures of the ITS2 region in the genus Tricholoma were identified for use in bioinformatic processes to study molecular evolution and compare secondary structures. Ten newly sequenced ITS regions were added to the analysis and submitted to the GenBank database. The resulting structure from a minimum energy algorithm indicated the four-domain model, as previously suggested by others. The conserved secondary structure of the ITS2 sequences of the genus Tricholoma exhibited certain unique features, including pyrimidine tracts in the loops of domain A and a complete structure containing four domains, with motifs identified in other ITS2 secondary structures. A phylogenetic tree was derived from sequence alignment based on the secondary structures. From the resulting maximum parsimonious tree, it was found that the species in the genus Tricholoma had evolved monophyletically and were composed of four groups, as supported by the bootstrapping values and pileus color.

• BMB Reports
• /
• 제38권4호
• /
• pp.440-446
• /
• 2005

A cDNA that was rapidly induced upon abscisic acid, cold, drought, mechanical wounding and to a lesser extent, by high salinity treatment, was isolated from Arabidopsis seedlings. It was classified as DREB subfamily member based on multiple sequence alignment and phylogenetic characterization. Since it encoded a protein with a typical ERF/AP2 DNA-binding domain and was closely related to the TINY gene, we named it TINY2. Gel retardation assay revealed that TINY2 was able to form a specific complex with the previously characterized DRE element while showed only residual affinity to the GCC box. When fused to the GAL4 DNA-binding domain, either full-length or its C-terminus functioned effectively as a trans-activator in the yeast one-hybrid assay while its N-terminus was completely inactive. Our data indicate that TINY2 could be a new member of the AP2/EREBP transcription factor family involved in activation of down-stream genes in response to environmental stress.

• 한국컴퓨터정보학회논문지
• /
• 제11권5호
• /
• pp.311-320
• /
• 2006

지식관리 전략은 비즈니스 기회의 창출과 유지에 핵심적인 요소로 인식되고 있다. 본 연구의 목적은 전자지급결제 영역에서의 지식관리의 역할을 지식공유 관점에서 분석하고, 다양한 전자지급결제방식에 적합한 지식공유 전략을 제시하는 것이다. 이를 위하여 전자지급결제의 특성을 결정짓는 2가지 요소인 신뢰성과 효율성을 기반으로 지식관리-전자지급결제 분류모형도를 제시하고, 각 영역에 적합한 지식공유 전략을 도출하였다. 연구의 결과에서 전자지급결제 특성과 지식공유 전략의 정합성이 전자지급결제 영역의 거래 당사자간의 관계 결속을 증가시키고 거래 과정을 최적화 시킬 수 있음을 제시하였다.

• Bulletin of the Korean Chemical Society
• /
• 제26권6호
• /
• pp.952-958
• /
• 2005

Angiotensin-converting enzyme (ACE) is known to be primarily responsible for hypertension. Threedimensional quantitative structure-activity relationship (3D-QSAR) models have been constructed using the comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) for a series of 28 ACE inhibitors. The availability of ACE crystal structure (1UZF) provided the plausible biological orientation of inhibitors to ACE active site (C-domain). Alignment for CoMFA obtained by docking ligands to 1UZF protein using FlexX program showed better statistical model as compared to superposition of corresponding atoms. The statistical parameters indicate reasonable models for both CoMFA ($q^2$ = 0.530, $r^2$ = 0.998) and CoMSIA ($q^2$ = 0.518, $r^2$ = 0.990). The 3D-QSAR analyses provide valuable information for the design of ACE inhibitors with potent activity towards C-domain of ACE. The group substitutions involving the phenyl ring and carbon chain at the propionyl and sulfonyl moieties of captopril are essential for better activity against ACE.

• 한국자기공명학회논문지
• /
• 제13권2호
• /
• pp.117-125
• /
• 2009

HP0062 is an 86 residue hypothetical protein from Helicobacter pylori strain 26695. HP0062 was identified ESAT-6/WXG100 superfamily protein based on structure and sequence alignment and also contains leucine zipper domain sequence. Here, we report the sequence-specific backbone resonance assignment of HP0062. About 97.7% of all $^1H_N,\;^{15}N,\;^{13}C_{\alpha},\;^{13}C_{\beta}\;and\;^{13}C=O$ resonances were assigned unambiguously. We could predict the secondary structure of HP0062 by analyzing the deviation of the $^{13}C_{alpha}\;and\;^{13}C_{\beta}$ chemical shifts from their respective random coil values. Secondary structure prediction shows that HP0062 consist of two ${\alpha}$-helices. This study is a prerequisite for determining the solution structure of HP0062 and can be used for the study on interaction between HP0062 and DNA and other Helicobacter pylori proteins.

• Journal of Plant Biotechnology
• /
• 제49권1호
• /
• pp.15-29
• /
• 2022

Cyclophilins (CYPs) are highly conserved ubiquitous proteins belong to the peptidyl prolyl cis/trans isomerase (PPIase) superfamily. These proteins are present in a wide range of organisms; they contain a highly conserved peptidyl-prolyl cis/trans isomerase domain. A comprehensive database survey identified a total of 35 genes localized in all cellular compartments of Solanum lycopersicum L., but largely in the cytosol. Sequence alignment and conserved motif analyses of the SlCYP proteins revealed a highly conserved CLD motif. Evolutionary analysis predicted the clustering of a large number of gene pairs with high sequence similarity. Expression analysis using the RNA-Seq data showed that the majority of the SlCYP genes were highly expressed in mature leaves and blooming flowers, compared with their expression in other organs. This study provides a basis for the functional characterization of individual CYP genes in the future to elucidate their role(s) in protein refolding and long-distance signaling in tomatoes and in plant biology, in general.

• Interdisciplinary Bio Central
• /
• 제1권2호
• /
• pp.8.1-8.6
• /
• 2009

Introduction: It is a challenge to design a protein score function which stabilizes the native structures of many proteins simultaneously. The coarse-grained description of proteins to construct the pairwise-contact score function usually ignores the backbone directionality of protein structures. We propose a new two-body score function which stabilizes all native states of 1,006 proteins simultaneously. This two-body score function differs from the usual pairwise-contact functions in that it considers two adjacent amino acids at two ends of each peptide bond with the backbone directionality from the N-terminal to the C-terminal. The score is a corresponding propensity for a directional alignment of two adjacent amino acids with their local environments. Results and Discussion: We show that the construction of a directional adjacency-score function was achieved using 1,006 training proteins with the sequence homology less than 30%, which include all representatives of different protein classes. After parameterizing the local environments of amino acids into 9 categories depending on three secondary structures and three kinds of hydrophobicity of amino acids, the 32,400 adjacency-scores of amino acids could be determined by the perceptron learning and the protein threading. These could stabilize simultaneously all native folds of 1,006 training proteins. When these parameters are tested on the new distinct 382 proteins with the sequence homology less than 90%, 371 (97.1%) proteins could recognize their native folds. We also showed using these parameters that the retro sequence of the SH3 domain, the B domain of Staphylococcal protein A, and the B1 domain of Streptococcal protein G could not be stabilized to fold, which agrees with the experimental evidence.

• 한국전자통신학회논문지
• /
• 제19권3호
• /
• pp.571-576
• /
• 2024

온톨로지는 도메인 전문가에 의해 만들어지지만, 동일한 내용이라도 전문가마다 도메인 지식에 대한 이해가 다르기 때문에 상이하게 표현될 수 있다. 아직 온톨로지 표준화가 부족하기 때문에 동일한 도메인 내에 여러 개의 온톨로지가 존재할 수 있으며, 이로 인해 온톨로지 이질성이라는 현상이 발생한다. 따라서 우리는 온톨로지 이질성 문제를 해결하기 위해 SCBOW(: Siames Continuois Bag Of Words)와 BERT(: BiDirectional Encoder Representations from Transformers) 모델을 결합한 새로운 온톨로지 매칭 방법을 제안한다. 온톨로지를 그래프로 표현하며, 온톨로지 매칭 문제에서 발생할 수 있는 일대다 문제를 해결하기 위해 SimRank 알고리즘을 사용한다. 실험 결과 우리의 접근 방식이 전통적인 매칭 알고리즘보다 약 8%의 성능 향상을 보였다. 제안 방법은 온톨로지 매칭에 사용되는 정렬 기술을 향상하고 개선할 수 있다.

• Nuclear Engineering and Technology
• /
• 제56권2호
• /
• pp.745-752
• /
• 2024

A method for gamma/neutron event classification based on frequency-domain analysis for mixed radiation environments is proposed. In contrast to the traditional charge comparison method for pulse-shape discrimination, which requires baseline removal and pulse alignment, our method does not need any preprocessing of the digitized data, apart from removing saturated traces in sporadic pile-up scenarios. It also features the identification of neutron events in the detector's full energy range with a single device, from thermal neutrons to fast neutrons, including low-energy pulses, and still provides a superior figure-of-merit for classification. The proposed frequency-domain analysis consists of computing the fast Fourier transform of a triggered trace and integrating it through a simplified version of the transform magnitude components that distinguish the neutron features from those of the gamma photons. Owing to this simplification, the proposed method may be easily ported to a real-time embedded deployment based on Field-Programmable Gate Arrays or Digital Signal Processors. We target an off-the-shelf detector based on a small CLYC (Cs2LiYCl6:Ce) crystal coupled to a silicon photomultiplier with an integrated bias and preamplifier, aiming at lightweight embedded mixed radiation monitors and dosimeter applications.

• 대한간호학회지
• /
• 제30권6호
• /
• pp.1411-1426
• /
• 2000

A nursing activity classification for hospitalized patients was performed based on an article review regarding nursing definition and nursing activity classification system. The study was conducted as follows: 1) Taxonomy was developed by the research team through the Delphi process and review article. The taxonomy consists of four nursing processes, (assessment, diagnosis, intervention and evaluation) and twelve nursing activity domains space (resperation, nutrition, elimination, exercise/alignment maintenance, comfort, hygiene, safety, spiritual support, counseling/ education, medication, communication, patient and information management). 2) First, nursing activities of the intervention process were listed and then classified by the nursing process of assessment, diagnosis, intervention and evaluation. The list consists of twelve nursing activity domains and 136 nursing activities. 3) A pilot study was conducted in two hospitals to verify validity and appropriateness of nursing activities. 4) The content validity index, which was calculated by 6 clinical practice experts, was 0.95. Also, a nursing activity classification system should also be developed in the department of community nursing and home health care nursing.