• Molecules and Cells
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• 제38권9호
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• pp.781-788
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• 2015

Mutations of MYO15A are generally known to cause severe to profound hearing loss throughout all frequencies. Here, we found two novel MYO15A mutations, c.3871C>T (p.L1291F) and c.5835T>G (p.Y1945X) in an affected individual carrying congenital profound sensorineural hearing loss (SNHL) through targeted resequencing of 134 known deafness genes. The variant, p.L1291F and p.Y1945X, resided in the myosin motor and IQ2 domains, respectively. The p.L1291F variant was predicted to affect the structure of the actin-binding site from three-dimensional protein modeling, thereby interfering with the correct interaction between actin and myosin. From the literature analysis, mutations in the N-terminal domain were more frequently associated with residual hearing at low frequencies than mutations in the other regions of this gene. Therefore we suggest a hypothetical genotype-phenotype correlation whereby MYO15A mutations that affect domains other than the N-terminal domain, lead to profound SNHL throughout all frequencies and mutations that affect the N-terminal domain, result in residual hearing at low frequencies. This genotype-phenotype correlation suggests that preservation of residual hearing during auditory rehabilitation like cochlear implantation should be intended for those who carry mutations in the N-terminal domain and that individuals with mutations elsewhere in MYO15A require early cochlear implantation to timely initiate speech development.

• Asian Pacific Journal of Cancer Prevention
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• 제13권1호
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• pp.69-73
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• 2012

Cancer is a complex disease and the genetic susceptibility to it could be an outcome of the inherited difference in the capacity of xenobiotic metabolizing enzymes. Glutathione-S-transferases (GSTs) are phase II metabolizing enzymes whose various genotypes have been associated with increased risk of different types of cancer. Null mutations caused by the deletion of the entire gene result in the absence of the enzymatic activity and increase in the risk of developing cancer including chronic myeloid leukaemia (CML). In the present case-control study we evaluated the effect of null mutations in GSTM1 and GSTT1 genes on the risk of developing CML. The study included 75 CML patients (43 males and 32 females; age (mean ${\pm}$ S.D) $42.3{\pm}13.4$ years) and unrelated non-malignant controls (76 male and 48 females; age (mean ${\pm}$ S.D) $41.5{\pm}12.9$). The distribution of GSTM1 and GSTT1 genotypes in CML patients and controls was assessed by multiplex-PCR method. Logistic regression was used to assess the relationship between GSTM1 and GSTT1 genotypes and risk of CML. Chi-square test was used to evaluate the trend in modulating the risk to CML by one or more potential high risk genotype. Although GSTM1 null genotype frequency was higher in CML patients (41%) than in the controls (35%), it did not reached a statistical significance (OD = 1.32, 95% CI: 0.73-2.40; P value = 0.4295). The frequency of GSTT1 null genotypes was higher in the CML patients (36%) than in the controls (21%) and the difference was found to be statistically significant (OD = 2.12, 95% CI: 1.12-4.02; P value = 0.0308). This suggests that the presence of GSTT1genotype may have protective role against the CML. We found a statistically significant (OD = 3.09, 95% CI: 1.122-8.528; P value = 0.0472) interaction between the GSTM1 and GSTT1 null genotypes and thus individuals carrying null genotypes of both GSTM1 and GSTT1 genes are at elevated risk of CML.

• 한국생물정보학회:학술대회논문집
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• 한국생물정보시스템생물학회 2005년도 BIOINFO 2005
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• pp.267-271
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• 2005

The goal of data mining is to extract new and useful knowledge from large scale datasets. As the amount of available data grows explosively, it became vitally important to develop faster data mining algorithms for various types of data. Recently, an interest in developing data mining algorithms that operate on graphs has been increased. Especially, mining frequent patterns from structured data such as graphs has been concerned by many research groups. A graph is a highly adaptable representation scheme that used in many domains including chemistry, bioinformatics and physics. For example, the chemical structure of a given substance can be modelled by an undirected labelled graph in which each node corresponds to an atom and each edge corresponds to a chemical bond between atoms. Internet can also be modelled as a directed graph in which each node corresponds to an web site and each edge corresponds to a hypertext link between web sites. Notably in bioinformatics area, various kinds of newly discovered data such as gene regulation networks or protein interaction networks could be modelled as graphs. There have been a number of attempts to find useful knowledge from these graph structured data. One of the most powerful analysis tool for graph structured data is frequent subgraph analysis. Recurring patterns in graph data can provide incomparable insights into that graph data. However, to find recurring subgraphs is extremely expensive in computational side. At the core of the problem, there are two computationally challenging problems. 1) Subgraph isomorphism and 2) Enumeration of subgraphs. Problems related to the former are subgraph isomorphism problem (Is graph A contains graph B?) and graph isomorphism problem(Are two graphs A and B the same or not?). Even these simplified versions of the subgraph mining problem are known to be NP-complete or Polymorphism-complete and no polynomial time algorithm has been existed so far. The later is also a difficult problem. We should generate all of 2$^n$ subgraphs if there is no constraint where n is the number of vertices of the input graph. In order to find frequent subgraphs from larger graph database, it is essential to give appropriate constraint to the subgraphs to find. Most of the current approaches are focus on the frequencies of a subgraph: the higher the frequency of a graph is, the more attentions should be given to that graph. Recently, several algorithms which use level by level approaches to find frequent subgraphs have been developed. Some of the recently emerging applications suggest that other constraints such as connectivity also could be useful in mining subgraphs : more strongly connected parts of a graph are more informative. If we restrict the set of subgraphs to mine to more strongly connected parts, its computational complexity could be decreased significantly. In this paper, we present an efficient algorithm to mine frequent subgraphs that are more strongly connected. Experimental study shows that the algorithm is scaling to larger graphs which have more than ten thousand vertices.

• 미생물학회지
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• 제46권1호
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• pp.80-85
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• 2010

보리 맥아로부터 발견된 서로 다른 알파아밀라제 동질효소(AMY1, AMY2)는 80%에 달하는 높은 아미노산 서열의 상동성을 보이지만, 두 효소의 특성은 서로 달라 AMY1 효소는 낮은 농도의 칼슘 조건에서 최대 활성을 보이는 반면, AMY2 효소는 높은 칼슘이온 농도에서 높은 활성을 나타낸다. 또한 BASI (Barley ${\alpha}$-Amylase/Subtilisin Inhibitor) 단백질은 AMY2 효소만을 특이적으로 저해한다. 따라서 본 연구에서는 AMY1과 AMY2 효소의 유전자를 I, II, III의 세 부위로 나눈 후, 제한효소 처리에 의해 일부 부위를 상호 치환한 4종의 chimera 효소를 추가로 제조하고, Pichia pastoris 균주에서 대량 발현하였다. 이들 효소의 특성을 비교한 결과, 제 I 부위만이 상호치환된 AMY211 및 AMY122 효소의 경우, AMY1과 AMY2의 중간적 칼슘 의존성을 나타내었으며, BASI에 의한 저해효과는 AMY2의 제 I, II 부위를 포함하는 AMY221 효소에서만 관찰되었다. 따라서 보리 아밀라제의 제 I 부위 및 제 II 부위에 존재하는 아미노산 잔기들이 칼슘 의존성 및 BASI와의 결합에 중요한 역할을 담당하는 반면 제 III 부위는 이들 효소의 활성 차이에 영향을 미치지 않음을 확인하였다.

• Journal of Applied Biological Chemistry
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• 제60권2호
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• pp.125-131
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• 2017

고창 부안 갯벌에 자생하는 칠면초의 근권 및 근면으로부터 내염성을 지니는 9 균주를 분리하였다. 16S rRNA 유전자를 이용한 계통분석으로 분리된 균주는 Vibrio 속과 Bacillus 속으로 분류되었다. 분리된 균주 중 Vibrio와 Bacillus로 나누어 각각 대표성을 나타낼 수 있는 균주를 선택하여 염 농도에 따른 최적 생장조건을 평가한 결과, 균주 JRS-1 (Vibrio neocaledonicus)은 총 염분 4-6%에서 높은 생장률을 보였다. 균주 JRL-2(Bacillus thuringiensis)는 염분 농도 증가에 따라 생장이 증가하였으며, 7%에서 최대 생장률을 보이고 8%에서는 감소하는 경향을 보였다. 분리된 균주들은 기존에 서식하던 토양의 염 농도인 3% (w/v) 보다 더 높은 염분에도 견딜 수 있는 내염성을 보였다. 또한 분리균주에 대한 생화학적 기질 이용 형태에 분석을 통해 triglyceride, ${\rho}$-nitrophenyl-${\alpha}$,$\text\tiny{D}$-glucoside, ${\rho}$-nitrophenyl-${\beta}$, $\text\tiny{D}$-glucoside 이용 등 식물과의 특이적인 상호작용을 나타내는 것으로 간주할 수 있는 반응들을 확인하였다.

• 환경생물
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• 제37권3호
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• pp.351-361
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• 2019

이매패류의 부유유생은 성패(양식자원)에 직접적인 영향을 미치고 있어, 부유유생의 출현시기 및 출현량에 관한 연구는 자연 채묘량의 증대와 인공종묘의 생산을 위해서 매우 중요하다. 이에 본 연구에서는 유전자 분석기법을 이용하여 보성 연안에서 총 21종의 이매패류 부유유생을 확인하였으며, 이 중 구마모토굴(M. sikamea), 왜홍합(X. atratus), 종밋(M. senhousia), 참굴(M. gigas), 가리맛 조개(S. constricta), 새꼬막(A. kagoshimensis), Kurtiella aff. bidentata 그리고 꼬막(T. granosa)이 중요 부유유생으로 관찰되었다. 특히, 보성 연안해역의 주요 수산자원인 새꼬막(A. kagoshimensis)과 꼬막(T. granosa)은 각각 이매패류의 0.51~12.50% (평균 4.00%), 0.01~12.50% (평균 1.92%)의 구성비율을 차지하며 다른 이매패류보다 낮은 출현량을 보였다. 꼬막(T. granosa)과 새꼬막(A. kagoshimensis)의 부유유생은 6월부터 9월까지 관찰되었으나, 각각 8월 초와 8월말에 가장 높은 출현율을 보였다.

• Journal of Microbiology and Biotechnology
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• 제25권11호
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• pp.1944-1953
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• 2015

A novel alkaline protease from Streptomyces sp. M30, SapHM, was purified by ammonium sulfate precipitation, hydrophobic interaction chromatography, and DEAE-Sepharose chromatography, with a yield of 15.5% and a specific activity of 29,070 U/mg. Tryptic fragments of the purified SapHM were obtained by electrospray ionization quadrupole time-of-flight mass spectrometry. Nucleotide sequence analysis revealed that the gene sapHM contained 1,179 bp, corresponding to 392 amino acids with conserved Asp156, His187, and Ser339 residues of alkaline protease. The first 24 amino acid residues were predicted to be a signal peptide, and the molecular mass of the mature peptide was 37.1 kDa based on amino acid sequences and mass spectrometry. Pure SapHM was optimally active at 80℃ in 50 mM glycine-NaOH buffer (pH 9.0), and was broadly stable at 0-50℃ and pH 4.0-9.0. The protease relative activity was increased in the presence of Ni²⁺, Mn²⁺, and Cu²⁺ to 112%, 113%, and 147% of control, respectively. Pure SapHM was also activated by dimethylformamide, dimethyl sulfoxide, Tween 80, and urea. The activity of the purified enzyme was completely inhibited by phenylmethylsulfonyl fluoride, indicating that it is a serine-type protease. The K_m and V_max values were estimated to be 35.7 mg/ml, and 5 × 10⁴ U/mg for casein. Substrate specificity analysis showed that SapH was active on casein, bovine serum albumin, and bovine serum fibrin.

• Asian Pacific Journal of Cancer Prevention
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• 제15권1호
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• pp.179-184
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• 2014

Chemoresistance of breast cancer to doxorubicin is mediated mainly through activation of NF-kB and over expression of HER2. Curcumin and its analogues (PGV-0 and PGV-1) exert cytotoxic effects on T47D breast cancer cells. Suppression of NF-kB activation is suggested to contribute to this activity. The present study aimed to explore the effects of curcumin, PGV-0, and PGV-1 singly and in combination with doxorubicin on MCF-7/Dox cells featuring over-expression of HER2. In MTT assays, curcumin, PGV-0, and PGV-1 showed cytotoxicity effects against MCF-7/Dox with IC50 values of $80{\mu}M$, $21{\mu}M$, and $82{\mu}M$ respectively. These compounds increased MCF-7/Dox sensitivity to doxorubicin. Cell cycle distribution analysis exhibited that the combination of curcumin and its analogues with Dox increased sub G-1 cell populations. Curcumin and PGV-1 but not PGV-0 decreased localization of p65 into the nucleus induced by Dox, indicating that activation of NF-kB was inhibited. Molecular docking of curcumin, PGV-0, and PGV-1 demonstrated high affinity to HER2 at ATP binding site. This interaction were directly comparable with those of ATP and lapatinib. These findings suggested that curcumin, PGV-0 and PGV-1 enhance the Dox cytotoxicity to MCF-7 cells through inhibition of HER2 activity and NF-kB activation.

• 한국균학회지
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• 제20권2호
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• pp.118-125
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• 1992

노랑느타리 Pleuroltus cornucopiae와 사철느타리 Pleurolus florida의 영양요구주(營養要求株)로부터 나출(裸出)한 원형질체(原形質體)를 polyethylene glycol로 융합(融合)하여 종간(種間) 체세포잡종(體細胞雜種)을 얻었다. 이들은 핵융합주(核融合株) nuclear hybrid 또는 이질이배체(異質二倍體) allodiploid, 이핵체(異核體) heterokaryon, 자연적(自然的) 분리성이핵체(分離性異核體) spontaneous segregated heterokaryon로 나누어졌으며, 6융합조합(融合組合)중에서 1조합(組合)에서만 꺽쇠연결체 clamp connection를 가진 것이 나타났다. 총 59 융합주 중에서 꺽쇠연결체를 가진 2균주와 가지지 않은 10균주가 완전한 자실체(子實體)를 형성하였는데 거의 사철느타리 형태(形態)와 유사(有似)하였으나 버섯의 갓 색택(色澤)이 양친(兩親)인 노랑느타리가 어릴때 yellow, 사철느타리가 orange white 인데비해 체세포 잡종은 light blond-greyish brown 으로 다양한 혼합색(混合色)으로 나타났다. 꺽쇠연결체가 없는 융합주로부터 발용(發茸)된 자실체는 두균주를 제외하고 모두 꺽쇠연결체를 가졌으며, 이 자실체(子實體) 조직(組織)을 완전배지(完全培地)에 배양(培養)한 결과 균사생장(菌絲生長)이 빠르고 균사도 꺽쇠연결체를 가져 본래(本來)의 융합주와는 다른 형태로 변하였다.

• 미생물학회지
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• 제48권2호
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• pp.125-133
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• 2012

혐기성 소화는 음식물 쓰레기와 같은 폐기물로부터 재생 가능한 에너지원으로 메탄을 생성하는 공정이다. 본 연구에서는 음식물 쓰레기와 폐수를 동시에 처리하는 3단계 메탄생산 공정을 이용한 혐기성 소화공정의 bacteria와 archaea 군집 변화를 조사하였다. 3단계 메탄생산 공정은 음식물 쓰레기 및 폐수를 메탄과 이산화탄소로 전환하는 반혐기성 가수분해/산생성, 혐기성 산생성과 혐기성 메탄생성조로 구성되어있으며, 16 rRNA 유전자 라이브러리의 염기서열 분석과 정량 PCR 등의 분자생물학적 방법으로 주요 미생물 군집을 조사하였다. 메탄생산 공정의 주요 미생물 군집은 VFA-산화 박테리아와 Methanoculleus 속에 속하는 hydrogenotrophic methanogen의 두 종(species)이었다. 또한, 소수의 Picrophilaceae 과(Thermoplasmatales 목)의 archaea도 확인하였다. 음식물을 이용한 3단계 메탄생산 공정은 acetogenesis를 기반으로 하는 고전적 메탄생성 공정과 달리 주로 hydrogenotrophic methanogen의 분해 경로에 의해 이루어 짐을 알 수 있다. 이들 균주의 우점은 중온 소화공정, 중성 pH, 높은 암모니아 농도, 짧은 HRT, Tepidanaerobacter 속 등과 같은 VFA 산화세균과의 상호작용 등에서 기인한 것으로 생각된다.