• Genomics & Informatics
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• 제21권2호
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• pp.21.1-21.14
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• 2023

Fusobacterium nucleatum is a gram-negative bacteria associated with diverse infections like appendicitis and colorectal cancer. It mainly attacks the epithelial cells in the oral cavity and throat of the infected individual. It has a single circular genome of 2.7 Mb. Many proteins in F. nucleatum genome are listed as "Uncharacterized." Annotation of these proteins is crucial for obtaining new facts about the pathogen and deciphering the gene regulation, functions, and pathways along with discovery of novel target proteins. In the light of new genomic information, an armoury of bioinformatic tools were used for predicting the physicochemical parameters, domain and motif search, pattern search, and localization of the uncharacterized proteins. The programs such as receiver operating characteristics determine the efficacy of the databases that have been employed for prediction of different parameters at 83.6%. Functions were successfully assigned to 46 uncharacterized proteins which included enzymes, transporter proteins, membrane proteins, binding proteins, etc. Apart from the function prediction, the proteins were also subjected to string analysis to reveal the interacting partners. The annotated proteins were also put through homology-based structure prediction and modeling using Swiss PDB and Phyre2 servers. Two probable virulent factors were also identified which could be investigated further for potential drug-related studies. The assigning of functions to uncharacterized proteins has shown that some of these proteins are important for cell survival inside the host and can act as effective drug targets.

• 생명과학회지
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• 제24권2호
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• pp.128-136
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• 2014

알긴산은 ${\alpha}$-L-guluronic acid와 ${\beta}$-D-mannuronic acid가 (1-4) 결합한 선형 산성다당류이다. 알긴산은 다양한 알긴산 분해효소들에 의하여 분해되는데 ${\beta}$-제거반응으로 비환원 말단에 이중결합이 있는 불포화 우론산 올리고머가 생산된다. 본 연구실에서는 이전에 Stenotrophomonas maltophilia KJ-2로부터 새로운 구조를 가진 polyMG lyase를 재조합하였다. KJ-2 polyMG lyase의 단백질구조를 예측하기 위하여 상동성 모델링을 한 결과 Azotobacter vinelandii가 생산하는 세 종류의 polyMG lyase들이 모두 PL7 family에 속하는 반면 KJ-2 polyMG lyase는 PL6 family에 속하였다. 또한 $^1H$-NMR spectra를 분석한 결과 polyMG lyase는 M-${\beta}$(1-4)-G 당쇄결합을 분해하고 G-${\alpha}$(1-4)-M 결합은 거의 분해하지 못하는 것으로 나타났다. 예측된 polyMG lyase 모델을 기초로 하여 14군데 아미노산 잔기를 선택하였으며 17개의 돌연변이체를 만들어 알긴산 분해효소의 활성을 측정하였다. Lys220Ala, Arg241Ala, Arg241Lys및 Arg265Ala 돌연변이체들은 완전히 알긴산 분해효소의 활성을 잃었으며 Arg155Ala, Gly303Glu 및 Tyr304Phe 돌연변이체들의 분해활성은 19.1-39.3%까지 감소하였다. 이러한 결과들로부터 Arg155, Lys220, Arg241, Arg265, Gly303 및 Tyr304 들은 알긴산 분해효소의 촉매활성과 기질결합에 중요한 잔기들임을 알 수 있다.

• BMB Reports
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• 제40권3호
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• pp.315-324
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• 2007

The novel $\alpha$-amylase purified from locally isolated strain, Bacillus sp. KR-8104, (KRA) (Enzyme Microb Technol; 2005; 36: 666-671) is active in a wide range of pH. The enzyme maximum activity is at pH 4.0 and it retains 90% of activity at pH 3.5. The irreversible thermoinactivation patterns of KRA and the enzyme activity are not changed in the presence and absence of $Ca^{2+}$ and EDTA. Therefore, KRA acts as a $Ca^{2+}$-independent enzyme. Based on circular dichroism (CD) data from thermal unfolding of the enzyme recorded at 222 nm, addition of $Ca^{2+}$ and EDTA similar to its irreversible thermoinactivation, does not influence the thermal denaturation of the enzyme and its Tm. The amino acid sequence of KRA was obtained from the nucleotide sequencing of PCR products of encoding gene. The deduced amino acid sequence of the enzyme revealed a very high sequence homology to Bacillus amyloliquefaciens (BAA) (85% identity, 90% similarity) and Bacillus licheniformis $\alpha$-amylases (BLA) (81% identity, 88% similarity). To elucidate and understand these characteristics of the $\alpha$-amylase, a model of 3D structure of KRA was constructed using the crystal structure of the mutant of BLA as the platform and refined with a molecular dynamics (MD) simulation program. Interestingly enough, there is only one amino acid substitution for KRA in comparison with BLA and BAA in the region involved in the calcium-binding sites. On the other hand, there are many amino acid differences between BLA and KRA at the interface of A and B domains and around the metal triad and active site area. These alterations could have a role in stabilizing the native structure of the loop in the active site cleft and maintenance and stabilization of the putative metal triad-binding site. The amino acid differences at the active site cleft and around the catalytic residues might affect their pKa values and consequently shift its pH profile. In addition, the intrinsic fluorescence intensity of the enzyme at 350 nm does not show considerable change at pH 3.5-7.0.

• Reproductive and Developmental Biology
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• 제35권1호
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• pp.105-113
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• 2011

The present study investigated the nuclear remodeling, development potential with telomerase activity and transcription level of X-linked genes (ANT3, HPRT, MeCP2, RPS4X, XIAP, XIST and ZFX) in the bovine somatic cell nuclear transfer (SCNT) embryos using two different fusion and activation methods. Female adult fibroblasts were injected into perivitelline space of in vitro matured oocytes. The oocyte-nucleus complexes were fused and followed by immediately either activated (Group 1), or activated at 1 h post-fusion (hpf) (Group 2), respectively. The incidence of normal premature chromosome condensation (PCC) at 1 hpf was slightly increased in the Group 2, compared to those of Group 1, but there was no significant (p<0.05) difference. The incidence of normal pronucleus (PN) and chromosome spread at 5 and 18 hpf were significantly (p<0.05) higher in the Group 2 than those of Group 1. The cleavage rate to 2-cell stage, developmental rate to blastocyst stage, and the mean number of total and ICM cell numbers were significantly (p<0.05) higher in the Group 2, compared to those of Group 1. Level of telomerase activity was significantly (p<0.05) higher in the SCNT blastocysts of Group 2, compared to those of Group 1. Transcript levels of HPRT, MeCP2 and XIST were not significantly (p<0.05) different between blastocysts of Group 1 and 2. However, transcript level of ANT3, RPS4X, XIAP and ZFX were significantly (p<0.05) up-regulated in the SCNT blastocysts of Group 2, compared to those of Group 1. Taken together, it is concluded that oocyte activation at 1 hpf induces the enhanced developmental potential by efficient nuclear remodeling and subsequent facilitation of the nuclear reprogramming of bovine SCNT embryos.

• 한국미생물·생명공학회지
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• 제34권2호
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• pp.129-135
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• 2006

Zebrafish (Danio rerio)의 microsomal epoxide hydrolase(mEH)로 추정되는 유전자를 클로닝하고 그 특성을 연구하였다. D. rerio의 mEH 추정단백질은 포유동물의 mEH 및 세균의 EH들과 아미노산서열 상동성을 보였으므로 결정분자구조(1qo7 및 1ehy)를 template로 하여 homology modelling을 행하였다. 클로된 단백질은 $Asp^{233}$, $Glu^{413}$ 및 $His^{440}$으로 구성된 catalytic triad와 2개의 tyrosine 잔기 및 oxyanion hole이 보존되어 있었다. 생물정보학적인 분석 및 EH 활성시험은 추정단백질이 D. rerio의 mEH라는 것을 보여주었다. Racemic styrene oxide를 기질로 하여 활성시험을 행한 결과, 재조합 D. rerio mEH는 (R)-styrene oxide을 입체선택적으로 가수분해하였으며 45분 반응시간에 99%ee의 광학순도를 가진 (S)-styrene oxide를 33.5% 얻을 수 있었다.

• 한국미생물학회:학술대회논문집
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• 한국미생물학회 2002년도 추계학술대회
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• pp.121-124
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• 2002

This work was initiated to develope a recombinant oral poliovaccine (OPV), which is highly advanced in safety (minimizing VAPP) by introducing Type 2,3 poliovirus epitopes into our RPS-Vax system. We have introduced several potential vaccine epitopes of poliovirus Type 2, and 3 into RPS-Vax system, resulting in production of recombinant polioviruses. Any of these chimeric viruses, however, were not detected for their foreign gene expression by serotype-specific mouse antiserum. We have designed several folding units to stabilize the introduced vaccine protein and attached short epitope-concatamer or epitope-multimer to them, followed by production of chimeric viruses. Only those who have an HIV-1 Tat-mediated folding unit were nicely detected for the introduced foreign proteins by anti-Tat antiserum and type-specific peptide-induced antisera. Nevertheless, introduced epitopes were not detected in Western blot experiment with each serotype-specific antiserum. None of the mice inoculated with these chimeric viruses showed preventative immunity when challenged with Lansing and Leon wildtype 2 and 3 poliovirus, and the antiserum did not show neutralizing capacity in vitro. Conformational epitope covering B/C loop region of type 2 and 3 were newly designed by computer modeling, and introduced into the RPS-Vax vector system, followed by production of chimeric viruses. Introduced epitope regions were nicely detected by anti-Tag23 mAb or peptide antibody, but still not detected by poliovirus antiserum. Nevertheless, neutralizing antibody was detected in the Tg-PVR mice even when inoculated once with these chimeric viruses. Also, the immunized mice showed perfect preventative immunity against the wild Type poliovirus Lancing or Leon. When boosted appropriately, those chimeric virus-inoculated Tg-PVR mice produced equivalent amounts of neutralizing antibody to those in Sabin 2/3-immunized mice. These data strongly suggest that our recombinant poliovirus (RPS-PV2 and RPS-PV3) can be used as a safe and effective rec-OPV instead of any preexisting poliovaccine.

• Journal of Microbiology and Biotechnology
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• 제25권1호
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• pp.89-97
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• 2015

Bacillus subtilis HK176 with high fibrinolytic activity was isolated from cheonggukjang, a Korean fermented soyfood. A gene, aprE176, encoding the major fibrinolytic enzyme was cloned from B. subtilis HK176 and overexpressed in E. coli BL21(DE3) using plasmid pET26b(+). The specific activity of purified AprE176 was 216.8 ± 5.4 plasmin unit/mg protein and the optimum pH and temperature were pH 8.0 and 40℃, respectively. Error-prone PCR was performed for aprE176, and the PCR products were introduced into E. coli BL21(DE3) after ligation with pET26b(+). Mutants showing enhanced fibrinolytic activities were screened first using skim-milk plates and then fibrin plates. Among the mutants, M179 showed the highest activity on a fibrin plate and it had one amino acid substitution (A176T). The specific activity of M179 was 2.2-fold higher than that of the wild-type enzyme, but the catalytic efficiency (k_cat/K_m) of M179 was not different from the wild-type enzyme owing to reduced substrate affinity. Interestingly, M179 showed increased thermostability. M179 retained 36% of activity after 5 h at 45℃, whereas AprE176 retained only 11%. Molecular modeling analysis suggested that the 176^th residue of M179, threonine, was located near the cation-binding site compared with the wild type. This probably caused tight binding of M179 with Ca²⁺, whichincreased the thermostability of M179.

• 한국수자원학회:학술대회논문집
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• 한국수자원학회 2007년도 학술발표회 논문집
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• pp.423-427
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• 2007

현재까지 하천의 흐름, 유사이동, 수질해석을 위해서는 외국에서 개발된 소프트웨어를 주로 사용해 오고 있었다. 학술 분야에서는 국내의 모형들이 연구되어졌지만 그에 따른 GUI나 가시화 시스템에 대한 실용화는 거의 이루어지지 못하였다. 본 연구에서는 범용 2차원 하천 흐름, 수질, 유사이동 해석을 위한 GUI 및 가시화 시스템(이하 RAMS, River Analysis and Modeling System)을 개발하여, 하상변동 및 오염물 이송확산에 미치는 수리학적 영향을 규명할 수 있도록 하였다. RAMS는 크게 mesh generator, 해석 모형의 입력 GUI 모듈, 입출력 파일 생성 모듈, 그리고 모의 결과의 가시화 시스템 등으로 이루어져 있다. Mesh generator는 지형자료(이미지 또는 DXF 파일)를 백그라운드 이미지로 가져올 수 있으며, 삼각형 노드와 사각형 노드를 지원한다. 또한 thin triangle들을 제거하는 기능, 선택된 요소(elements)를 제거하는 기능, triangle들을 서로 병합하여 사각형 요소를 만드는 기능, mesh의 renumbering 기능 등을 구현하였다. 특히 사용자가 잘못 생성한 요소들을 바로 이전 상태로 환원하는 undo/redo 기능을 구현하여 능률적인 mesh 생성이 가능하다. 해석 모형의 입력 GUI 모듈에는 각 해석 모형(흐름, 수질, 유사이동)에 특화된 GUI를 설계하여 사용자는 보다 친숙한 환경에서 편리하게 자료를 입력할 수 있다. 입출력 파일 생성 모듈에서는 사용자가 GUI를 통해 입력한 자료를 파일로 변환하여 즉각적으로 모의를 수행하며, 그 출력 파일을 읽어 모의 결과를 자동적으로 가시화한다. 모의 결과의 가시화 시스템에서는 수많은 모의 결과를 체계화하여 등고선 및 화살표 등으로 표현하며, time step 별 결과를 바로 확인할 수 있다. 또한 애니메이션 기능을 구현하여 사용자가 원하는 구간의 time step에서의 모의 결과를 연속적으로 볼 수 있으며, 이 애니메이션을 AVI 파일로 변환하여 다른 동영상 프로그램에서도 재생할 수 있다. 본 연구에서 개발한 RAMS를 이용하여 하천 설계 시 그 공학적 근거를 제시하고, 국내 실정에 맞는 국산 소프트웨어를 제공함으로써 하천의 흐름, 수질, 유사이동 해석에 의한 하천의 수리학적 거동을 보다 편리하고 정확하게 모의할 수 있을 것으로 기대된다.

• 디지털융복합연구
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• 제17권8호
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• pp.429-437
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• 2019

본 연구는 전주시에 거주하는 베이비부머의 다양한 자본역동과 역동이 삶의 질에 미치는 영향을 확인했다. 더불어 초기와 후기베이비부머로 구분되는 출생코호트의 조절효과를 검증했다. 검증을 위해 303 베이비부머를 대상으로 구조방정식모델링을 적용했다. 연구결과는 첫째, 베이비부머의 인적자본은 심리자본, 경제자본, 사회자본, 삶의 질에 직간접 영향을 미쳤다. 둘째, 경제자본은 심리자본, 사회자본, 삶의 질에 직간접 영향을 미쳤다. 셋째, 심리자본은 사회자본, 삶의 질에 직간접 영향을 미쳤다. 넷째, 사회자본은 삶의 질에 직접 영향을 미쳤다. 다섯째, 출생코호트는 경제자본이 심리자본과 삶의 질에 미치는 영향을 조절했다. 검증된 자원역동과 조절효과는 베이비부머의 삶의 질에 대한 이해와 중재방향을 제공했다. 향후 연구지역을 농촌과 대도시로, 연구대상을 베이비붐 이후세대로 확장을 권고한다.

• Journal of Veterinary Science
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• 제22권1호
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• pp.12.1-12.11
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• 2021

Background: Bats have been considered natural reservoirs for several pathogenic human coronaviruses (CoVs) in the last two decades. Recently, a bat CoV was detected in the Republic of Korea; its entire genome was sequenced and reported to be genetically similar to that of the severe acute respiratory syndrome CoV (SARS-CoV). Objectives: The objective of this study was to compare the genetic sequences of SARS-CoV, SARS-CoV-2, and the two Korean bat CoV strains 16BO133 and B15-21, to estimate the likelihood of an interaction between the Korean bat CoVs and the human angiotensin-converting enzyme 2 (ACE2) receptor. Methods: The phylogenetic analysis was conducted with the maximum-likelihood (ML) method using MEGA 7 software. The Korean bat CoVs receptor binding domain (RBD) of the spike protein was analyzed by comparative homology modeling using the SWISS-MODEL server. The binding energies of the complexes were calculated using PRODIGY and MM/GBGA. Results: Phylogenetic analyses of the entire RNA-dependent RNA polymerase, spike regions, and the complete genome revealed that the Korean CoVs, along with SARS-CoV and SARS-CoV-2, belong to the subgenus Sarbecovirus, within BetaCoVs. However, the two Korean CoVs were distinct from SARS-CoV-2. Specifically, the spike gene of the Korean CoVs, which is involved in host infection, differed from that of SARS-CoV-2, showing only 66.8%-67.0% nucleotide homology and presented deletions within the RBD, particularly within regions critical for cross-species transmission and that mediate interaction with ACE2. Binding free energy calculation revealed that the binding affinity of Korean bat CoV RBD to hACE2 was drastically lower than that of SARS-CoV and SARS-CoV-2. Conclusions: These results suggest that Korean bat CoVs are unlikely to bind to the human ACE2 receptor.