• BMB Reports
• /
• 제40권4호
• /
• pp.588-594
• /
• 2007

A novel hot spring thermophile, Anoxybacillus gonensis A4 (A. gonensis A4) was investigated in terms of capability of tributyrin degradation and characterization of its thermostable esterase activity by the hydrolysis of p-nitrophenyl butyrate (PNPB). It was observed that A. gonensis A4 has an esterase with a molecular weight of 62 kDa. The extracellular crude preparation was characterized in terms of substrate specificity, pH and temperature optima and stability, kinetic parameters and inhibition/activation behaviour towards some chemicals and metal ions. Tributyrin agar assay showed that A. gonensis A4 secreted an esterase and $V_{max}$ and $K_m$ values of its activity were found to be 800 U/L and 176.5 ${\mu}M$, respectively in the presence of PNPB substrate. The optimum temperature and pH, for A. gonensis A4 esterase was $60-80^{\circ}C$ and 5.5, respectively. Although the enzyme activity was not significantly changed by incubating crude extract solution at $30-70^{\circ}C$ for 1 h, the enzyme activity was fully lost at $80^{\circ}C$ for same incubation period. The pH-stability profile showed that original crude esterase activity increased nearly 2-fold at pH 6.0. The effect of some chemicals on crude esterase activity indicated that A. gonensis A4 produce an esterase having serine residue in active site and -SH groups were essential for its activity.

• Neonatal Medicine
• /
• 제25권3호
• /
• pp.102-108
• /
• 2018

Purpose: Congenital diaphragmatic hernia (CDH) is rare but potentially fatal. The overall outcome is highly variable. This study aimed to identify a simple and dynamic parameter that helps predict the mortality of CDH patients in real time, without invasive tests. Methods: We conducted a retrospective chart review of 59 CDH cases. Maternal and fetal information included the gestational age at diagnosis, site of defect, presence of liver herniation, and lung-to-head ratio (LHR) at 20 to 29 weeks of gestational age. Information regarding postnatal treatment, including the number of days until surgery, the need for inhaled nitric oxide (iNO), the need for extracorporeal membrane oxygenation (ECMO), and survival, was collected. The highest respiratory severity score (RSS) within 24 hours after birth was also calculated. Results: Statistical analysis showed that a younger gestational age at the initial diagnosis (P<0.001), a lower LHR (P=0.001), and the presence of liver herniation (P=0.003) were prenatal risk factors for CDH mortality. The RSS and use of iNO and ECMO were significant factors affecting survival. In the multivariate analysis, the only remaining significant risk factor was the highest preoperative RSS within 24 hours after birth (P=0.002). The area under the receiver operating characteristic curve was 0.9375, with a sensitivity of 91.67% and specificity of 83.87% at the RSS cut-off value of 5.2. The positive and negative predictive values were 82.14% and 92.86%, respectively. Conclusion: Using the RSS as a prognostic predictor with simple calculations will help clinicians plan CDH management.

• Journal of Microbiology and Biotechnology
• /
• 제24권2호
• /
• pp.160-167
• /
• 2014

Oligopeptidase B (OpdB) is a serine peptidase widespread among bacteria and protozoa that has emerged as a virulence factor despite its function has not yet been precisely established. By using an OpdB-overexpressing Escherichia coli strain, we found that the overexpressed peptidase makes the bacterial cells specifically less susceptible to several proline-rich antimicrobial peptides known to penetrate into the bacterial cytosol, and that its level of activity directly correlates with the degree of resistance. We established that E. coli OpdB can efficiently hydrolyze in vitro cationic antimicrobial peptides up to 30 residues in length, even though they contained several prolines, shortening them to inactive fragments. Two consecutive basic residues are a preferred cleavage site for the peptidase. In the case of a single basic residue, there is no cleavage if proline residues are present in the $P_1$ and $P_2$ positions. These results also indicate that cytosolic peptidases may cause resistance to antimicrobial peptides that have an intracellular mechanism of action, such as the proline-rich peptides, and may contribute to define the substrate specificity of the E. coli OpdB.

• 분석과학
• /
• 제10권5호
• /
• pp.378-385
• /
• 1997

본 실험은 human glutathione S-transferase P1-1의 tyrosine 7 잔기에 대한 변이체를 작성하고, 기질특이성과 저해제의 효과를 조사하여, 이 잔기의 기능을 분석한 것이다. 1,2-dichloro-4-nitrobenzene과 1,2-epoxy-3-(p-nitrophenoxy)propane에 대한 GSH 포합반응에 대한 활성은 야생형에 비해 변이체 Y7F에서는 3~5%로 크게 저하하였으며, 효소에 결합한 GSH의 thiol기의 pKa는 2.4 pK 높았다. 저해제 hematin에 대한 $I^{50}$값은 야생형과 변이체 Y7F에서 비슷하게 나타났으며, 저해제 benastatin A와 S-(2,4-dinitrophenyl) glutathione에 대한 $I^{50}$값들은 다소 감소하였다. 이러한 결과들로부터 tyrosine 7 잔기는 기질의 결합에 관여하기보다 GSH-chloronitrobenzene 유도체와 GSH-epoxide 포함반응에 대한 촉매활성에 중요하다고 생각된다.

• Environmental Analysis Health and Toxicology
• /
• 제16권2호
• /
• pp.97-102
• /
• 2001

FMOs (Flavin-containing monooxygenases, EC1.14.13.8)는 다양한 종류의 식품, 약물이나 기타 외래 유래물질 (xenobiotics)를 산화시키는 NADPH와 $O_2$ 의존성 약물대사효소이다. 현재까지 5종의 subfamily가 존재하는 것으로 보고되어 있으며 그 중 잘 알려진 FMO3는 대표적 인 subfamily로서 주로 간에 존재한다 사람FMO에 관한 연구는 최근 들어 활성화되기 시작했으며 질소, 황이나 인 등을 포함하는 친핵성 (nucleophilic) 화합물이 대표적인 기질로 보고되어 있다. 본 연구에서는 thiocarbamide를 포함하고 있는 화합물에 대한 사람의 FMO3의 기질 특이성을 알아보고자 하였다. 사람 FMO3를 baculovirus system을 이용하여 대량으로 발현시킨 후 그 microsomal FMO3를 분리하여 thiocholine assay를 시행하였다. 그 결과 methimazole, thiourea, and phenylthiourea는 낮은 $K_{m}$ (4-10$\mu$M)간을 갖는 반면, 이보다 기질의 크기가 큰 1 ,3-diphenylthiourea, 1, 3-bis (3, 4-dichlorophenyl)-2-thiourea, 1, 1-dibenzyl-3-phenol-2-thiourea에서는 효소활성이 나타나지 않았다. 이는 사람 fM01과 비교하여 볼 때 큰 차이는 없었으며, 다른 pig, guinea pig, rat, rabbit에서 보다 받아들일 수 있는 기질의 크기가 더 제한적임을 알 수 있었다.

• 한국정보과학회논문지:소프트웨어및응용
• /
• 제36권10호
• /
• pp.851-860
• /
• 2009

최근 계산을 통한 단백질 상호작용 예측 기법 중, 단백질 쌍이 포함하고 있는 도메인들 사이의 관계에 중점을 둔 도메인 정보 기반 예측 기법들이 다양하게 제안되고 있다. 하지만, 다수의 도메인 쌍들이 상호작용에 기여하는 정도를 정밀하게 반영하는 계산 기법은 드문 실정이다. 본 논문에서는 단백질 상호작용에 있어 도메인 조합 쌍의 상호작용 영향력을 수치화하여 반영한 상호작용 중요도 행렬을 고안하고 이를 기반으로 한 단백질 상호작용 예측 시스템을 구현한다. 일반적인 도메인 조합 기법과 달리, 상호작용 중요도 행렬에서는 상호작용을 위한 도메인간의 협업 확률이 고려된 Weighted 도메인 조합과, 다수의 Weighted 도메인 조합 중 실제 상호작용 주체가 될 확률을 도메인 조합 쌍의 힘(Domain Combination Pair Power, DCPPW)으로 수치화한다. DIP과 IntAct에서 얻어온 S. cerevisiae의 단백질 상호작용 데이터와 Pfam-A 도메인 정보를 사용한 정확도 검증 결과, 평균 63%의 민감도와 94%의 특이도를 확인하였으며, 학습집단의 증가에 따른 안정적인 예측 정확도 향상을 보였다. 본 논문에서 구현한 예측 시스템과 학습 데이터는 웹(http://code.google.com/p/prespi)을 통하여 내려 받을 수 있다.

• Journal of Microbiology and Biotechnology
• /
• 제21권5호
• /
• pp.529-535
• /
• 2011

Single-chain variable fragment (scFv) is a fusion protein of the variable regions of the heavy (VH) and light (VL) chains of immunoglobulin, connected with a short linker peptide of 10 to about 20 amino acids. In this study, the scFv of a monoclonal antibody against the third domain of human CD4 was cloned from OKT4 hybridoma cells using the phage display technique and produced in E. coli. The expression, production, and purification of anti-CD4 scFv were tested using SDS-PAGE and Western blot, and the specificity of anti-CD4 scFv was examined using ELISA. A 31 kDa recombinant anti-CD4 scFv was expressed and produced in bacteria, which was confirmed by SDS-PAGE and Western blot assays. Sequence analysis proved the ScFv structure of the construct. It was able to bind to CD4 in quality ELISA assay. The canonical structure of anti-CD4 scFv antibody was obtained using the SWISS_MODEL bioinformatics tool for comparing with the scFv general structure. To the best of our knowledge, this is the first report for generating scFv against human CD4 antigen. Engineered anti-CD4 scFv could be used in immunological studies, including fluorochrome conjugation, bispecific antibody production, bifunctional protein synthesis, and other genetic engineering manipulations. Since the binding site of our product is domain 3 (D3) of the CD4 molecule and different from the CD4 immunological main domain, including D1 and D2, further studies are needed to evaluate the anti-CD4 scFv potential for diagnostic and therapeutic applications.

• 농업과학연구
• /
• 제37권3호
• /
• pp.435-449
• /
• 2010

Soils in the sloping uplands in Korea are subject to intensive land use with high input of agrochemicals and are vulnerable to soil erosion. Development of the environmentally sound land management strategy is essential for a sustainable production system in the sloping upland. This report addresses the status of upland agriculture and the best management practices for the uplands toward the sustainable agriculture. More than 60% of Korean lands are forest and only 21% are cultivating paddy and upland. Uplands are about 7% of the total lands and about 62% of the uplands are in the slopes higher than 7%. Due to the site-specificity of the upland, many managerial and environmental problems are occurring, such as severe erosion, shallow surface soils with rocky fragments, and loadings of non-point source (NPS) contaminants into the watershed. Based on the field trials, most of the sloping uplands were classified as Suitability Class III-V and the major limiting factor was slope and rock fragments. Due to this, soils were over-applied with N fertilizer, even though N rate was the recommendation. This resulted in decreases in yield, degradation of soil quality and increases in N loading to the leachate. Various case studies drew management practices toward sustainable production systems. The suggested BMP on the managerial, vegetative, and structural options were to practice buffer strips along the edges of fields and streams, winter cover crop, contour and mulching farming, detention weir, diversion drains, grassed waterway, and slope arrangement. With these options, conservation effects such as reductions in raindrop impact, flow velocity, runoff and sediment loss, and rill and gully erosion were observed. The proper management practice is a key element of the conservation of the soil and water in the sloping upland.

• Genomics & Informatics
• /
• 제3권1호
• /
• pp.15-23
• /
• 2005

Background MicroRNAs (miRNAs) are a class of noncoding RNAs found in various organisms such as plants and mammals. However, most of the mRNAs regulated by miRNAs are unknown. Furthermore, miRNA targets in genomes cannot be identified by standard sequence comparison since their complementarity to the target sequence is imperfect in general. In this paper, we propose a kernel-based method for the efficient prediction of miRNA targets. To help in distinguishing the false positives from potentially valid targets, we elucidate the features common in experimentally confirmed targets. Results The performance of our prediction method was evaluated by five-fold cross-validation. Our method showed 0.64 and 0.98 in sensitivity and in specificity, respectively. Also, the proposed method reduced the number of false positives by half compared with TargetScan. We investigated the effect of feature sets on the classification of miRNA targets. Finally, we predicted miRNA targets for several miRNAs in the Caenorhabditis elegans (C. elegans) 3' untranslated region (3' UTR) database. Condusions The targets predicted by the suggested method will help in validating more miRNA targets and ultimately in revealing the role of small RNAs in the regulation of genomes. Our algorithm for miRNA target site detection will be able to be improved by additional experimental­knowledge. Also, the increase of the number of confirmed targets is expected to reveal general structural features that can be used to improve their detection.

• 대한한의학회지
• /
• 제22권2호
• /
• pp.109-119
• /
• 2001

Objective : There are many reports that acupuncture has thermoregulatory effects on human and animals. To investigate the effect and mechanism of antipyretic action of acupuncture, we observed the body temperature and cytokine expressions in the hypothalamus of rats. Methods : Lipopolysaccharide (LPS, i.p., 2.5mg/kg) was injected to conscious rats (Sprague-Dawley, male, n=4l) to cause hyperthermia and simple needling (stainless steel, 0.25 mm o.d., 5 mm insertion for 10 sec with no manipulation) was performed bilaterally with the measurement of rectal temperature. Next, we sacrificed rats to remove brain and determined the level of mRNA for interleukin-6 (IL-6), $interleukin-1{\beta}{\;}(IL-1{\beta})$, interleukin-2 (IL-2) and $interferon-{\gamma}{\;}(IFN-{\gamma})$ in the hypothalamus by using reverse transcriptase-polymerase chain reaction (RT-PCR). Resul1s : Needling on forepaw (acupoint HT8) and needling on hindpaw (acupoint BL66 and acupoint LR2) significantly inhibited LPS-induced fever of rats (P<0.01, 10 min after treatment respectively), but same treatment on proximal tail (non-acupoint) did not cause any change on fever. The levels of IL-6 and $IL-1{\beta}$ mRNA in the hypothalamus was significantly enhanced by LPS-injection, while the level of IL-6 and $IL-1{\beta}$ mRNA was markedly reduced after treatment on BL66 (P<0.01). Treatment on forepaw reduced it slightly, but not significantly. Equivalent stimulation on proximal tail did not cause any changes. Conclusions : Our results indicate that acupuncture stimulation on various body parts has differential thermoregulatory effects on LPS-induced fever of rats with site-specificity. And, we suggest that its antipyretic action might be accompanied with the suppression of hypothalamic production of pro-inflammatory cytokine of immune system, IL-6 and $IL-1{\beta}$.