• 대한전자공학회:학술대회논문집
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• 대한전자공학회 1999년도 하계종합학술대회 논문집
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• pp.474-478
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• 1999

Genetic algorithm is an efficient search method using principles of natural selection and population genetics. In conventional genetic algorithms, however, the size of gene pool should be increased to insure a convergency. Therefore, many memory spaces and much computation time were needed. Also, since child chromosomes were generated by chromosome crossover and gene mutation, the algorithms have a complex structure. Thus, in this paper, a compact stereo matching algorithm using a population-based incremental teaming based on probability vector is proposed to reduce these problems. The PBIL method is modified for matching environment. Since the Proposed algorithm uses a probability vector and eliminates gene pool, chromosome crossover, and gene mutation, the matching algorithm is simple and the computation load is considerably reduced. Even if the characteristics of images are changed, stable outputs are obtained without the modification of the matching algorithm.

• Bulletin of the Korean Chemical Society
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• 제27권5호
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• pp.657-662
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• 2006

Identification of accessible sites in targeted RNAs is a major limitation to the effectiveness of antisense oligonucleotides. A class of antisense oligodeoxynucleotides, known as the “10-23” DNA enzyme or DNAzyme, which is a small catalytic DNA, has been shown to efficiently cleave target RNA at purine-pyrimidine junctions in vitro. We have designed a strategy to identify accessible cleavage sites in the target RNA, which is hepatitis C virus nonstructural gene 3 (HCV NS3) RNA that encodes viral helicase and protease, from a pool of random DNAzyme library. A pool of DNAzymes of 58 nucleotides-length that possess randomized annealing arms, catalytic core sequence, and fixed 5'/3'-end flanking sequences was designed and screened for their ability to cleave the target RNA. The screening procedure, which includes binding of DNAzyme pool to the target RNA under inactive condition, selection and amplification of active DNAzymes, incubation of the selected DNAzymes with the target RNA, and target site identification on sequencing gels, identified 16 potential cleavage sites in the target RNA. Corresponding DNAzymes were constructed for the selected target sites and were tested for RNA-cleavage in terms of kinetics and accessibility. These selected DNAzymes were effective in cleaving the target RNA in the presence of $Mg^{2+}$. This strategy can be applicable to identify accessible sites in any target RNA for antisense oligonucleotides-based gene inactivation methods.

• Plant Biotechnology Reports
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• 제4권3호
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• pp.201-211
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• 2010

We present a highly effective T-DNA inserted gene screening method as part of a reverse genetics model system using the Chinese cabbage (Brassica rapa L. spp. pekinensis). Three-step two-dimensional (2D) matrix strategies are potentially accurate and useful for the identification of specific T-DNA inserted mutants from a large population. To construct our Chinese cabbage model, we utilized a forward genetics screening approach for the abnormal phenotypes that were obtained from transgenic plants of Brassica rapa generated with Agrobacteria tumefaciens containing the pRCV2 vector. From one transgenic plant with an abnormal phenotype, we observed that the st1 gene (which is related to senescence-associated process proteins) contained a T-DNA fragment, and that its expression level was decreased. This T-DNA insert was then used as a control to construct an effective screening pool. As a result, the optimum template concentration was found to be 0.1-1 ng in our PCR strategy. For other conditions, positive changes to the Gibbs free energy prevented the formation of oligo dimers and hairpin loop structures, and autosegment extension gave better results for long fragment amplification. Using this effective reverse genetics screening method, only 23 PCR reactions were necessary to select a target gene from a pool of 100 individual DNAs. Finally, we also confirmed that the sequence we obtained from the above method was identical to the flanking sequence isolated by rescue cloning.

• 전자공학회논문지S
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• 제36S권10호
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• pp.103-112
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• 1999

유전 알고리즘은 적절한 해를 찾기 위해서 자연선택과 개체군 유전학을 이용한 효율적 탐색기법이다. 그러나, 기존의 유전 알고리즘들은 수렴을 보장하기 위해서 유전자 풀의 크기를 증가시켜야 했고 그 결과 저장공간과 계산 시간이 많이 소요되었다. 또한, 염색체 교차와 유전자 돌연변이를 사용하여 새로운 염색체를 발생시켰기 때문에 알고리즘이 복잡하다는 단점이 있다. 본 논문에서는 이런 문제를 줄이기 위해서 확률벡터에 기반한 개체기반 증가 학습이라는 소형 유전 알고리즘을 정합 환경에 맞게 변형시킨 새로운 스테레오 정합 방법을 제안하였다. 제안된 알고리즘은 확률벡터의 사용으로 인해 유전 풀, 염색체 교차, 그리고 유전자 돌연변이 연산을 제거하였다. 그 결과 제안된 정합 알고리즘은 기존 방식보다 구조가 간단하고 계산량의 향상이 있었으며, 영상의 특성에 상관없이 안정된 결과를 얻을 수 있다는 장점이 있었다.

• The Plant Pathology Journal
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• 제39권5호
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• pp.417-429
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• 2023

Ralstonia solanacearum species complex (RSSC) is a soil borne plant pathogen causing bacterial wilt on various important crops, including Solanaceae plants. The bacterial pathogens within the RSSC produce exopolysaccharide (EPS), a highly complicated nitrogencontaining heteropolymeric polysaccharide, as a major virulence factor. However, the biosynthetic pathway of the EPS in the RSSC has not been fully characterized. To identify genes in EPS production beyond the EPS biosynthetic gene operon, we selected the EPS-defective mutants of R. pseudosolanacearum strain SL341 from Tn5-inserted mutant pool. Among several EPSdefective mutants, we identified a mutant, SL341P4, with a Tn5-insertion in a gene encoding a putative NDP-sugar epimerase, a putative membrane protein with sugar-modifying moiety, in a reverse orientation to EPS biosynthesis gene cluster. This protein showed similar to other NDP-sugar epimerases involved in EPS biosynthesis in many phytopathogens. Mutation of the NDP-sugar epimerase gene reduced EPS production and biofilm formation in R. pseudosolanacearum. Additionally, the SL341P4 mutant exhibited reduced disease severity and incidence of bacterial wilt in tomato plants compared to the wild-type SL341 without alteration of bacterial multiplication. These results indicate that the NDP-sugar epimerase gene is required for EPS production and bacterial virulence in R. pseudosolanacearum.

• 한국생물공학회:학술대회논문집
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• 한국생물공학회 2005년도 생물공학의 동향(XVI)
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• pp.317-321
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• 2005

L- arabinose residues are widely distributed in plant cell walls, where they are present in polymers such as arabinans, arabinoxylans, arabinogalactans and arabinogalactan proteins. L-arabinose suppress intestinal sucrase and decrease the adsorption of sugar in the small intestine, consequently, weight loss and fatness prevent. Now, xylose be used replacement sugar and arabinose be utilized fatness prevent of our time. Various Agricultural surplus like com fiber, contain $20\;{\sim}\;40%$ of hemicellulose. Corn fiber from Agricultural Renewable Biomass was chosen the best suitable material for arabinose production. In this work, we searched about for L-arabinose gene in compost, metagenome pool and indonesian soil. So, the B1029 TS2-8 of L-arabinase gene in compost was selected by YNB media(5% yeast nitrogen base, 5% arabinogalactan). After enzyme reaction with corn fiver, B1029 TS2-8 produced 2.15 g/L of L-arabonose.

• 한국미생물생명공학회:학술대회논문집
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• 한국미생물생명공학회 2001년도 Proceedings of 2001 International Symposium
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• pp.77-80
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• 2001

A variety of different methods to generate diverse proteins, including random mutagenesis and recombination, are currently available, and most of them accumulate the mutations on the target gene of a protein, whose sequence space remains unchanged. On the other hand, a pool of diverse genes, which is generated by random insertions, deletions, and exchange of the homologous domains with different lengths in the target gene, would present the protein lineages resulting in new fitness landscapes. Here we report a method to generate a pool of protein variants with different sequence spaces by employing green fluorescent protein (GFP) as a model protein. This process, designated functional salvage screen (FSS), comprises the following procedures： a defective GFP template expressing no fluorescence is firstly constructed by genetically disrupting a predetermined region(s) of the protein, and a library of GFP variants is generated from the defective template by incorporating the randomly fragmented genomic DNA from E. coli into the defined region(s) of the target gene, followed by screening of the functionally salvaged, fluorescence-emitting GFPs. Two approaches, sequence-directed and PCR-coupled methods, were attempted to generate the library of GFP variants with new sequences derived from the genomic segments of E. coli. The functionally salvaged GFPs were selected and analyzed in terms of the sequence space and functional property. The results demonstrate that the functional salvage process not only can be a simple and effective method to create protein lineages with new sequence spaces, but also can be useful in elucidating the involvement of a specific region(s) or domain(s) in the structure and function of protein.

• Journal of Microbiology and Biotechnology
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• 제20권7호
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• pp.1156-1162
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• 2010

During ethanol fermentation, bacterial strains may encounter various stresses, such as ethanol and acid shock, which adversely affect cell viability and the production of ethanol. Therefore, ethanologenic strains that tolerate abiotic stresses are highly desirable. Bacteria of the genus Deinococcus are extremely resistant to ionizing radiation, ultraviolet light, and desiccation, and therefore constitute an important pool of extreme resistance genes. The irrE gene encodes a general switch responsible for the extreme radioresistance of D. radiodurans. Here, we present evidence that IrrE, acting as a global regulator, confers high stress tolerance to a Zymomonas mobilis strain. Expression of the gene protected Z. mobilis cells against ethanol, acid, osmotic, and thermal shocks. It also markedly improved cell viability, the expression levels and enzyme activities of pyruvate decarboxylase and alcohol dehydrogenase, and the production of ethanol under both ethanol and acid stresses. These data suggest that irrE is a potentially promising gene for improving the abiotic stress tolerance of ethanologenic bacterial strains.

• 한국지능시스템학회:학술대회논문집
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• 한국퍼지및지능시스템학회 1995년도 추계학술대회 학술발표 논문집
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• pp.98-103
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• 1995

In this paper, a method is presented for finding an optimal temperature control pattern in microwaveoven using genetic algorithm. Power spectrum of temperature variance of charcoal is obtained and oven system modeling with fuzzy-neural-network is explained. Fan on/off timing is converted to strings in gene pool and then genetic iterations make the power spectrum of simmulated temperature variance of microwave oven closer to that o charcoal.

• 한국산림과학회지
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• 제83권2호
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• pp.191-204
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• 1994

삼림의 급격한 황폐화의 원인은 지구 환경의 악화와 무분별한 목재 자원의 남벌에 있다. 이러한 대규모의 삼림자원의 파괴에 의해 사라져가는 삼림 면적의 크기도 중요하지만 그에 못지 않게 그 안에 들어있는 식물종이 감소되어 가고 멸종되어 가는 것이 더욱 큰 문제가 된다. 이러한 종의 감소나 멸종이 가시적인 것이라고 한다면 종내의 유전변이의 감소는 눈에 보이지는 않지만 진화과정에 있어서 종을 유지하는데 필수적인 유전자 변이 폭이 좁아지기 때문에 매우 심각한 문제가 된다. 재배작물에 있어서 유전자 보존은 육종을 위한 측면에서 중요한 연구분야로 인식되어 왔다. 그러나 야생종인 삼림의 경우에는 현재 인간이 육종에 필요한 최소한의 개체만 유지 보존함으로써 유전변이가 심하게 축소되어 지속적으로 생존 진화할 수 있는 기본적 유전자 변이를 잃어버리게 될 위험에 처할 수 있기 때문에 삼림의 유전자보존이 절대적으로 필요한 것이다. 현재의 삼림 유전자 보존 정책은 현지보존, 현지외 보존, 시설내 보존으로 나누어 수행하고 있는데 아직도 그 방법이 확정되어 있지 않아서 많은 시행착오를 거듭하고 있다. 특히 광범위하게 분포되어 있는 같은 종의 삼림내 임목들간의 유전자변이를 조사 분석할 적당한 방법이 없으며 (동위효소변이에 많은 것을 의존하고 있으나 동위효소변이만으로 충분하지 못하다), 현지보존의 경우에도 얼마나 큰 집단을 또 어떤 행태로 보존해야 하는가에 대한 집단유전학적 이론 정립이 완전하지 못하다. 또한 현지외 보존의 경우 현지보존림의 유전변이를 빠짐없이 포함되도록 조성해야 할 구체적인 방법을 알지 못하고 있는 실정에 있다. 시설내 보존의 경우 종자 보관이나 화분 보관과 같은 기술적인 것은 재배작물의 방법을 적용하면 되지만 어떤 집단의 종자나 화분을 채집 보관해야 하는지에 대한 집단유전학적 근거가 아직 확실히 마련되고 있지 않다. 시설내 보존인 경우 기왕에 육종에 의해 선발된 개체를 유전자형(개체) 상태로 보존함으로써 부가가치를 높일 수 있을 것이며, 이러한 연구는 새롭게 개발되고 있는 조직배양 및 유전공학적 기법을 이용하므로써 발전할 수 있는 여지가 많은 연구 분야이다. 현지보존의 경우 유전자 보존만의 목적으로 조성된 삼림뿐만 아니라 다른 목적으로 보호 받고 있는 많은 삼림, 예를 들면 국립, 도립공원, 보안림, 노거수 등에 대한 적절한 생태유전학적인 연구를 통하여 유전자원으로 이용할 수 있는 방법이 강구되어야 하며, 현지외 보존의 경우에도 유전자원 보존림의 조성 뿐만 아니라 임목육종과정에서 기 조성되어 있는 채종원, 산지시험림, 차대검정림, 클론보존원 등에 대해서도 적절한 유전학적 연구 조사를 수행함으로써 현지외 유전자 보존림으로 이용할 수 있게 될 것이다.