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Evaluation of DNA Extraction Methods from Low Copy Number (LCN) DNA Samples for Forensic DNA Typing

  • Eom, Yong-Bin
    • Biomedical Science Letters
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    • v.15 no.3
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    • pp.229-232
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    • 2009
  • DNA isolation for PCR-based short tandem repeat (STR) analysis is essential to recover high yields of amplifiable DNA from low copy number (LCN) DNA samples. There are different methods developed for DNA extraction from the small bloodstain and gloves, commonly found at crime scenes. In order to obtain STR profiles from LCN DNA samples, DNA extraction protocols, namely the automated $iPrep^{TM}$ $ChargeSwitch^{(R)}$ method, the automated $QIAcube^{TM}$ method, the automated $Maxwell^{(R)}$ 16 DNA $IQ^{TM}$ Resin method, and the manual $QIAamp^{(R)}$ DNA Micro Kit method, were evaluated. Extracted DNA was quantified by the $Quantifiler^{TM}$ Human DNA Quantification Kit and DNA profiled by $AmpFISTR^{(R)}$ $Identifiler^{(R)}$ Kit. Results were compared based on the amount of DNA obtained and the completeness of the STR profiles produced. The automated $iPrep^{TM}$ $ChargeSwitch^{(R)}$ and $QIAcube^{TM}$ methoas produced reproducible DNA of sufficient quantity and quality trom the dried blood spot. This two automated methods showed a quantity and quality comparable to those of the forensic manual standard protocols normally used in our laboratory. In our hands, the automated DNA extraction method is another obvious choice when the forensic case sample available is bloodstain. The findings of this study indicate that the manual simple modified $QIAamp^{(R)}$ DNA Micro Kit method is best method to recover high yields of amplifiable DNA from the numerous potential sources of LCN DNA samples.

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A DNA Sequence Generation Algorithm for Traveling Salesman Problem using DNA Computing with Evolution Model (DNA 컴퓨팅과 진화 모델을 이용하여 Traveling Salesman Problem를 해결하기 위한 DNA 서열 생성 알고리즘)

  • Kim, Eun-Gyeong;Lee, Sang-Yong
    • Journal of Korean Institute of Intelligent Systems
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    • v.16 no.2
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    • pp.222-227
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    • 2006
  • Recently the research for Traveling Salesman Problem (TSP) using DNA computing with massive parallelism has been. However, there were difficulties in real biological experiments because the conventional method didn't reflect the precise characteristics of DNA when it express graph. Therefore, we need DNA sequence generation algorithm which can reflect DNA features and reduce biological experiment error. In this paper we proposed a DNA sequence generation algorithm that applied DNA coding method of evolution model to DNA computing. The algorithm was applied to TSP, and compared with a simple genetic algorithm. As a result, the algorithm could generate good sequences which minimize error and reduce the biologic experiment error rate.

DNA Computing Adopting DNA coding Method to solve Traveling Salesman Problem (Traveling Salesman Problem을 해결하기 위한 DNA 코딩 방법을 적용한 DNA 컴퓨팅)

  • Kim, Eun-Gyeong;Yun, Hyo-Gun;Lee, Sang-Yong
    • Journal of Korean Institute of Intelligent Systems
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    • v.14 no.1
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    • pp.105-111
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    • 2004
  • DNA computing has been using to solve TSP (Traveling Salesman Problems). However, when the typical DNA computing is applied to TSP, it can`t efficiently express vertices and weights of between vertices. In this paper, we proposed ACO (Algorithm for Code Optimization) that applies DNA coding method to DNA computing to efficiently express vertices and weights of between vertices for TSP. We applied ACO to TSP and as a result ACO could express DNA codes which have variable lengths and weights of between vertices more efficiently than Adleman`s DNA computing algorithm could. In addition, compared to Adleman`s DNA computing algorithm, ACO could reduce search time and biological error rate by 50% and could search for a shortest path in a short time.

The Bacteriophage λ DNA Replication Protein P Inhibits the oriC DNA- and ATP-binding Functions of the DNA Replication Initiator Protein DnaA of Escherichia coli

  • Datta, Indrani;Sau, Subrata;Sil, Alok Kumar;Mandal, Mitai C.
    • BMB Reports
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    • v.38 no.1
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    • pp.97-103
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    • 2005
  • Under the condition of expression of $\lambda$ P protein at lethal level, the oriC DNA-binding activity is significantly affected in wild-type E. coli but not in the rpl mutant. In purified system, the $\lambda$ P protein inhibits the binding of both oriC DNA and ATP to the wild-type DnaA protein but not to the rpl DnaA protein. We conclude that the $\lambda$ P protein inhibits the binding of oriC DNA and ATP to the wild-type DnaA protein, which causes the inhibition of host DNA synthesis initiation that ultimately leads to bacterial death. A possible beneficial effect of this interaction of $\lambda$ P protein with E. coli DNA initiator protein DnaA for phage DNA replication has been proposed.

CEO's Innovation DNA and Innovation : Fit of Environment (경영자 혁신DNA와 혁신 : 환경 적합성)

  • Kim, Seung Ho;Huh, Moo Yul
    • Asia-Pacific Journal of Business Venturing and Entrepreneurship
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    • v.10 no.1
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    • pp.95-110
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    • 2015
  • Most innovation related theories including entrepreneurship theory regard the CEO's innovative competencies as the starting point of innovation. The study was investigated the relationship between CEO's innovation DNA and Innovation and the effects of environmental fit in their relation. For the empirical test, the sample was collected from 110 manufacturing companies in Daegu and Gyeongbook region. The results as follows: First, Innovation DNA has generally significant positive effect on innovation. The effect of discovery DNA is stronger than operating DNA to the product innovation, but the operating DNA stronger than the discovery DNA to the process innovation. The fit between CEO's innovative DNA and exogenous environmental turbulence make a strength innovation. The supplementary fit between discovery DNA and technology turbulence and complementary fit between discovery DNA and market turbulence reinforce product innovation. Process innovation were strengthen by the complementary fit between operating DNA and market turbulence.

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Enviromental Toxic Agents on Genetic Material and Cellular Activity III. DNA Polymerase Inhibitors on Repair of Mutagen-Induced DNA Damage in Mammalian Cells (환경성 유해요인이 유전물질과 세포활성에 미치는 영향 III. 포유동물세포에서 돌연변이원에 의한 DNA 상해의 회복에 미치는 DNA 중합효소저해제의 영향)

  • 엄경일;선우양일;이천복;신은주
    • Environmental Mutagens and Carcinogens
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    • v.8 no.1
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    • pp.1-12
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    • 1988
  • The effects of aphidicolin (APC), an inhibitor of DNA polymerase alpha, or 2', 3'-dideoxythymidine 5'-triphosphate (ddTTP), an inhibitor of DNA polymerase beta, on the repair of DNA damage induced by ethyl methanesulfonate (EMS) or bleomycin (BLM) were investigated in Chinese hamster ovary (CHO)-K1 cells. Three assays were employed in this study: unscheduled DNA synthesis, alkaline elution and alkaline sucrose gradient sedimentation. It was shown that APC or ddTTP inhibited DNA induced by EMS, and thus, the post-treatment with APC or ddTTP following EMS treatment was resulted in the more amount of unscheduled DNA synthesis, and the more accumulation of DNA single-stand breaks than the cells post-incubated without APC or ddTTP. While, in the BLM induced DNA repair, only ddTTP inhibited DNA repair induced by BLM. And thus, the groups post-incubated with or without APC after BLM treatment had the same value in the amount of unscheduled DNA synthesis and of DNA single-strand breaks, while post-treatment with ddTTP was resulted in the increased amount of unscheduled DNA synthesis and the increased DNA sin -strand breaks than the group without ddTTP. These results suggested that both of DNA polymerase $\alpha$ and $\beta$ participated in the repair of DNA damage induced by EMS, but in BLM-induced DNA repair, polymerase $\beta$ participated.ipated.

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DNA Computing Adopting DNA Coding Method to solve Maximal Clique Problem (Maximal Clique Problem을 해결하기 위한 DNA 코딩 방법을 적용한 DNA 컴퓨팅)

  • Kim, Eun-Kyoung;Lee, Sang-Yong
    • The KIPS Transactions:PartB
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    • v.10B no.7
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    • pp.769-776
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    • 2003
  • DNA computing has used to solve MCP (Maximal Clique Problem). However, when current DNA computing is applied to MCP. it can't efficiently express vertices and edges and it has a problem that can't look for solutions, by misusing wrong restriction enzyme. In this paper we proposed ACO (Algorithm for Code Optimization) that applies DNA coding method to DNA computing to solve MCP's problem. We applied ACO to MCP and as a result ACO could express DNA codes of variable lengths and generate codes without unnecessary vertices than Adleman's DNA computing algorithm could. In addition, compared to Adleman's DNA computing algorithm, ACO could get about four times as many as Adleman's final solutions by reducing search time and biological error rate by 15%.

Evaluation of two DNA extraction methods on exhumed bone samples: Ultrafiltration versus column affinity (유골에서 DNA 추출법 비교 연구: Ultrafiltration과 Column affinity)

  • Kim, Soonhee;Hong, Seungbeom;Kemp, Brian M.;Park, Kiwon;Han, Myunsoo
    • Analytical Science and Technology
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    • v.21 no.4
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    • pp.338-343
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    • 2008
  • Extraction of DNA from skeletal material is of great importance in the identification of human remains, but is particularly difficult because the high amount of microbial DNA was often co-extracted with human bone DNA. We found that a phenol/chloroform extraction, followed by ultrafiltration, and cleanup by via the $QIAquick^{(R)}$ PCR purification kit yields higher amounts of human genomic DNA compared with extraction by the column affinity $method^{(R)}$ alone. Ultrafiltration extraction of human DNA from ten exhumed bone samples yielded $0.041-1.120ng/{\mu}L$ DNA (mean = $0.498ng/{\mu}L$ DNA), and purification using the column affinity resulted in $0.016-0.064ng/{\mu}L$ DNA (mean = $0.034ng/{\mu}L$ DNA). Although the STR genotyping by the column affinity method was partially successful, all DNA samples by the ultrafiltration method produced full profiles from the multiplex PCR. The efficiency of STR genotyping was in accordance with the amounts of the human DNA extracted.

A DNA Sequence Alignment Algorithm Using Quality Information and a Fuzzy Inference Method (품질 정보와 퍼지 추론 기법을 이용한 DNA 염기 서열 배치 알고리즘)

  • Kim, Kwang-Baek
    • Journal of Intelligence and Information Systems
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    • v.13 no.2
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    • pp.55-68
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    • 2007
  • DNA sequence alignment algorithms in computational molecular biology have been improved by diverse methods. In this paper, we proposed a DNA sequence alignment algorithm utilizing quality information and a fuzzy inference method utilizing characteristics of DNA sequence fragments and a fuzzy logic system in order to improve conventional DNA sequence alignment methods using DNA sequence quality information. In conventional algorithms, DNA sequence alignment scores were calculated by the global sequence alignment algorithm proposed by Needleman-Wunsch applying quality information of each DNA fragment. However, there may be errors in the process for calculating DNA sequence alignment scores in case of low quality of DNA fragment tips, because overall DNA sequence quality information are used. In the proposed method, exact DNA sequence alignment can be achieved in spite of low quality of DNA fragment tips by improvement of conventional algorithms using quality information. And also, mapping score parameters used to calculate DNA sequence alignment scores, are dynamically adjusted by the fuzzy logic system utilizing lengths of DNA fragments and frequencies of low quality DNA bases in the fragments. From the experiments by applying real genome data of NCBI (National Center for Biotechnology Information), we could see that the proposed method was more efficient than conventional algorithms using quality information in DNA sequence alignment.

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Expression of DNA-dependent Protein Kinase and Its Relationship with Epidermal Growth Factor Receptor Signaling in Metastatic Cancer Cell Lines (DNA-PK 및 표피성장인자수용체의 신호전달이 암전이에 미치는 영향)

  • Hwang Jee Young;Kim Sun Hee;Kang Chi Dug;Yoon Man Soo
    • Journal of Life Science
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    • v.15 no.3
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    • pp.406-414
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    • 2005
  • The genetic instability of cancer cells may be related to inappropriately activated DNA repair pathways. In present study, the modulated expression of DNA-dependent protein kinase (DNA-PK), a major DNA repair protein, in human cancer metastatic cells was tested. The expressions of Ku70/80, regulatory subunit of DNA-PK, and the Ku DNA-binding activity in various highly metastatic cell lines were higher than those in each parental cell line. Also, the expression of DNA-PKcs, catalytic subunit of DNA-PK, and the kinase activity of the whole DNA-PK complex in highly metastatic cells were significantly increased as compared to those of parental cells, suggesting that the enhanced DNA repair capacity of metastatic cells could be associated with aberrant use of DNA repair, which may mediate tumor progression and metastatic potential. Increased EGFR (epidermal growth factor receptor) signaling has been associated with tumor invasion and metastasis, and the linkage between EGFR-mediated signaling and DNA-PK has been suggested. This study showed that PKI166, the new EGFR tyrosine kinase inhibitor, modulated the expressions of Ku70/80 and DNA-PKcs and also revealed the chemosensitization effect of PKI166 against metastatic cells may be in part due to inhibition of Ku70/80. These results suggest that interference in EGFR signaling by EGFR inhibitor resulted in the impairment of DNA repair activity, and thus DNA-PK could be possible molecular targets for therapy against metastatic cancer cells.