• Journal of KIISE:Computing Practices and Letters
• /
• v.16 no.3
• /
• pp.275-280
• /
• 2010

A local alignment algorithm finds a substring pair of given two strings where two substrings of the pair are similar to each other. A DNA sequence can consist of not only A, C, G, and T but also N and X where N and X are used when the original bases lose their information for various reasons. In this paper, we present an efficient local alignment algorithm for two DNA sequences including N and X using the affine gap penalty metric. Our algorithm is an extended version of the Kim-Park algorithm and can be extended in case of including other characters which have similar properties to N and X.

• Journal of Internet Computing and Services
• /
• v.19 no.2
• /
• pp.1-7
• /
• 2018

Due to advances in DNA sequencing technologies, its medical value continues to grow. However, once genome data leaked, it cannot be revoked, and disclosure of personal genome information impacts a large group of individuals. Therefore, secure techniques for managing genomic big data should be developed. We first propose a privacy-preserving inner product protocol for large data sets using the homomorphic encryption of Gentry et al., and then we introduce an efficient privacy-preserving DNA matching protocol based on the proposed protocol. Our efficient protocol satisfies the requirements of correctness, confidentiality, and privacy.

• Journal of Life Science
• /
• v.24 no.2
• /
• pp.112-117
• /
• 2014

We investigated the effects of extracts from Rubus coreanus (RC) and Artemisia princeps var. orientalis (AP) on DNA damage response in ultraviolet B (UVB)-exposed HaCaT cells. Cell activity upon treatment for 24 h with RC or AP alone was similar to or greater than that of the nontreated control. When UVB-exposed cells were postincubated for 24 h in medium containing RC or AP, cell activity increased in a concentration-dependent manner. Nuclear fragmentation analysis showed that postincubation with RC or AP decreased UVB-induced apoptosis by about 20% and 15%, respectively, of that in cells postincubated with growth medium. When UVB-exposed cells were postincubated for 24 h in medium containing RC or AP, the level of cyclobutane pyrimidine dimer decreased in a concentration- dependent manner. Western blot analysis showed that treatment of cells not exposed to UVB with RC or AP alone did not significantly change the levels of phospho-p53 and GADD45 protein. Interestingly, when UVB-exposed cells were postincubated for 24 h in medium containing RC or AP, phospho-p53 and GADD45 levels decreased in a concentration dependent manner. Our results suggest that RC and AP extract assist the survival of UVB-exposed cells in parallel with a decrease in levels of UVB-induced DNA damage and damage-response proteins, such as p53 and GADD45.

• KOREAN JOURNAL OF CROP SCIENCE
• /
• v.37 no.5
• /
• pp.397-404
• /
• 1992

The mitotic cycle duration(MCD) and component phase periods of rice(Oryza sativa L.) root meristem cells on the different salt concentrations were investigated by using of tritiated thymidine. The time interval between the maxima of sequential mitotic appearances of marked cells was used as criteria in measuring the MCD of rice. The MCD of rice cultivars 'Seomjinbyeo and Chilseongbyeo' at 0.0%, 0.3%, and 0.6% of salt concentrations appeared the same period as 12hr. The durations of component phase of rice cultivar 'Seomjinbyeo' were the almost same periods at 0.1%, 0.3%, and 0.6% of salt, but in 'Chilseongbyeo' cultivar the G1 and G2 periods were shorter while the S period was longer at 0.3% and 0.6% of salt. Deoxyribonucleic acid(DNA) and protein synthesis were increased while ribonucleic acid(RNA) synthesis was decreased with increasing salt concentrations at Chilseombyeo roots. In Seomjinbyeo roots, DNA and RNA synthesis were decreased while protein synthesis was increased with increasing salt concentrations. These results suggest that DNA, RNA, and protein synthesis may not affect the MCD in rice, but the increase of protein synthesis may be related to the salt tolerance of rice.

• Proceedings of the Korean Information Science Society Conference
• /
• 2003.10b
• /
• pp.766-768
• /
• 2003

인간 및 다른 생물들의 DNA 서열이 밝혀짐에 따라 DNA 서열 정보를 이용할 수 있는 계산적 처리방식에 대한 요구가 늘어나고 있다. 본 논문에서는 DNA의 패턴을 분류할 수 있는 면역계 부정 선택에 기반한 알고리즘을 제안한다. 부정 선택은 면역세포 생성시 자신을 인식하지 않는 항원 인식부를 생성하기 위한 과정이다. 이 항원 인식부를 통해 자기와 비자기를 구별한다. 이것을 n개의 자기 또는 비자기 집단으로 확장하고 n개의 항원 집단을 구성하면 n개의 패턴 분류가 가능하다. 본 논문에서는 부정 선택에 기반한 DNA 염기 레벨에서의 패턴 분류방법과 아미노산 레벨에서의 패턴분류 방법을 제안한다.

• Microbiology and Biotechnology Letters
• /
• v.17 no.6
• /
• pp.539-544
• /
• 1989

Campylobacter jejuni, bacterial agent causing human diarrhea, were studied for their disinfection effects with chlorine and monochloramine. The cells treated with the chemical agents were observed by scanning electron microscopy to know their morphological and structural changes. The proteins and DNA in the chemical-treated cells were also examined by gel electrophoresis for structural changes. When C. jejuni were chlorinated at concentrations of 0.5 and 1.0 mg/l for 15 minutes, the organisms were disinfected by 4 and 6 log, respectively. Those disinfection effects were higher at acidic pH, while lowered at neutral and alkaline values of pH. The effects of monochloramine were lower than those of chlorine at the game concentration for the same period of reaction time. The shapes of C. jejuni cells treated with the agents appeared to be deformed from spiral rod into spherical forms, showing some destruction in surface structure of the cells. Some of the proteins and DNA of the chlorinated cells did not appear in the gel electrophoresis when the chlorination was at concentration of 10 mg/l or higher.

• Journal of the Society of Cosmetic Scientists of Korea
• /
• v.24 no.1
• /
• pp.87-99
• /
• 1998

We have studied the effects of red ginseng root extract on the derease of MMS-induced gemotoxicity in cultured NIH3T3 cells. The increase in survival and the recovery from DNA synthesis inhibition in MMS-treated cells as a function of normal medium incubation time was potentiated, at a rate higher than those in UV-irradiated cells, by the presence of the ginseng extract. The extract also increased the MMS-induced excision repair as determined by unscheduled DNA synthesis. The amount of MMS-induced DNA single strand breads that are accumulated by polymerase inhibitors was increased, but as a rate lower rate than in UV-induced strand break, by the presence of the extract. These results suggest that the red ginseng extract increase MMS-induced repair and could be used as a reagent for protectiong alkylating agent-induced genotoxicity and cytotoxicity.

• Proceedings of the KSAR Conference
• /
• 2001.03a
• /
• pp.21-21
• /
• 2001

일반적으로 세포는 방사능이나 항암제 등의 자극에 의해 DNA가 손상받았을 때 DNA를 합성하기 전, DNA변이를 복구하기 위해 cell cycle을 정지시키게 된다. pRB(retinoblatoma protein)는 이러한 cell cycle의 조절기작에서 중요한 역할을 담당하는 것으로 알려져 있다. G1기에서 S기로 진행하는 것을 조절하는 단백질인 pRB 은 E2F(cell cycle transcription factor)와 상호작용하여 cell cycle 진행에 필요한 전사활성을 억제, PCNA (proliferating cell nuclear antigen)의 합성을 저해한다. 또한, E2F와 결합된 pRB는 apoptosis를 제어하는 유전자를 조절하는 것으로 알려져 있다. Cell cycle에 영향을 미치는 항암제의 일종인 busulfan을 처리하면, 정소 내에 존재하는 대부분의 생식세포들은 사멸되고 spermatogonia만 남는 것으로 알려져 있다. 그러나 그 기작에 대해서는 자세히 연구된 바가 없다. 본 연구에서는 busulfan처리시 spermatogonial stem cell이 어떤 기작에 의해 손상받지 않고 유지되는지를 알아보고자 실험을 수행하였다. Busulfan을 처리한 마우스 (항암제 투여 후 5주)와 정상적인 13주령의 마우스의 정소로부터 각각 세포를 분리하였다. LSC (laser scanning cytometry)를 이용하여 처리군(busulfan treated mice)과 대조군(normal mature mice)에 대해 각각 DNA함량을 비교ㆍ분석한 결과 G0/G1(2N)에 머물러 있는 세포비율이 처리군에서 현저하게 증가했다 (79.3$\pm$5.5%:8.1$\pm$1.3%). Cell cycle의 G1/S check point인 pRB와 PCNA 발현을 Western blot과 면역조직학적인 방법(immunohisto-chemistry)을 이용하여 조사하였다 PCNA는 대조군과 비교해, 처리군에서 매우 낮은 수준으로 발현되었다. 면역염색된 정소단면을 살펴보면, 대조군에서는 모든 세정관에서 PCNA를 발현하는 세포가 높은 비율로 검출되었고, 처리군에서는 소수의 세정관에서 세포들이 낮은 수준으로 검출되었다. 반면에, pRB의 경우 PCNA와는 상반된 결과를 나타내어, 대조군에서는 거의 발현이 되지 않는 반면, 처리군에서는 대부분의 세정관내, 기저막을 따라 위치한 세포들에서 발현되었다. 이상의 결과는 busulfan에 의해 pRB의 인산화가 억제, pRB 와 결합된 E2F는 전사 활성이 억제되어, PCNA 합성을 저해하는 것으로 설명되어질 수 있다. 결론적으로, 인산화가 억제된 pRB (underphosphorylated RB protein)이 quiescent spermatogonial stem cell에서만 특이하게 발현하는 단백질이며, 이러한 pRB의 발현은 apoptosis를 제어하는 역할을 담당해 busulfan처리에 의해 손상받지 않고 남아있는 것으로 시사된다.

• The Magazine of the IEIE
• /
• v.29 no.3
• /
• pp.58-70
• /
• 2002

약 1그램의 DNA는 10/sup 21/개의 DNA 염기를 가지며 이것은 10억 terabits의 정보저장 능력에 해당한다. 분자정보처리기술(molecular information processing technology)은 DNA나 단백질과 같은 거대분자의 초미세구조, 초고집적도, 초에너지 소비특성에 기반하여, 용액상에서 아보가드로수(6×10/sup 23/) 규모의 분자들이 3차원 화학 반응에 관여하는 초병렬분산 정보 저장 및 처리 능력을 활용하는 차세대 IT 기술이다. 이는 또한 생체분자의 특성을 나노수준에서 활용하는 정보기술이라는 점에 있어서 BT+NT+IT의 융합기술이며 그 기술적 산업적인 파급 효과가 아주 큰 특징이 있다. 본고에서는 현재 분자정보 처리 기술의 원리 및 문제점을 설명하고 이의 해결을 위한 5가지 핵심 요소 기술을 도출한다. 최근 세계적인 연구 동향을 살펴보고, 국내의 기술 기반 및 국제 경쟁력을 분석하며, 궁극적인 경제성 확보를 위한 산업화 방안을 단기(3-5년), 중기(5-10년), 장기(10-20년)의 3단계로 나뉘어 제안한다.

• Biomedical Science Letters
• /
• v.3 no.1
• /
• pp.11-20
• /
• 1997

A regulation of differentiation in human neuroblastoma cells remains poorly understood, although it is of great importance in the clinical therapy of neuroblastoma. This study was aimed to elucidate effects of DNA synthesis inhibitors on the differentiation of neuroblastoma cells on the basis of morphological, biochemical and molecular respects. Three DNA synthesis inhibitors, sodium butyrate, hydroxyurea, cytosine arabinoside were used to explore their effects on the cellular morphology, the expression of c-myc and the elevation of choline acetyltransferase activity. They led to the extension or neurite-like processes reflecting differentiation or IMR-32 cells. In addition, the treatment of three DNA synthesis inhibitors resulted in the remarkable increases in the expression of c-myc as well as the stimulation of choline acetyltransferase activity which is involved in the synthesis of acetylcholine in the differentiated cholinergic neurons. Taken together, these results indicate that DNA synthesis inhibitors play an important role in the induction of cellular differentiation in IMR-32 cells. Furthermore these DNA synthesis inhibitors seem to be future useful to give an important clue (for the treatment of neuroblastoma).