• 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.

• Proceedings of the Korean Institute of Information and Commucation Sciences Conference
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• 2013.05a
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• pp.1012-1014
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• 2013

DNA-DNA hybridization method with four oligonucleotide-specific probes was used simultaneously for differentiation and identification of four Mycobacterium species (Mycobacterium tuberculosis, M. avium, M. intracellulare, and M. kansasii). This DNA-DNA hybridization method with 4 oligonucleotide-specific probes, which targets in the rpoB region of 4 Mycobacteria species, respectively, was tested on 322 clinical isolates. Using DNA-DNA hybridization method, we detected M. tuberculosis (282 strains), M. avim (7 strains), M. intracellulare (9 strains), and M. kansasii (3 strain) from 322 clinical isolates. This result was compared with conventional biochemical test and rpoB DNA sequence analysis of this clinical isolates. We confirmed identification of Mycobacterium tuberculosis, M. avium, M. intracellulare, and M. kansasii with high sensitivity (100 %) and specificity (100 %). This DNA-DNA hybridization method could be performed within 4 hours at least. Therefore, we suggest that DNA- DNA hybridization method using 4 rpoB DNA probes of Mycobacteria could be used for accurate, rapid, convenient detection and identification of Mycobacterium tuberculosis, M. avium, M. intracellulare, and M. kansasii in clinical samples.

• Journal of the Korean Institute of Intelligent Systems
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• v.13 no.6
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• pp.737-742
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• 2003

In this paper, we propose a new wavelet-based fuzzy modeling using a DNA coding method. Generally, it is well known that the DNA coding method is more diverse in the knowledge expression and better in the optimization performance than the genetic algorithm (GA) because it can encode more plentiful genetic information based on the biological DNA. The proposed method makes a fuzzy model by using the wavelet transform, in which coefficients are identified by the DNA coding method. Thus we can effectively get the fuzzy model of nonlinear system by using the advantages of both wavelet transform and DNA coding method. In order to demonstrate the superiority of the proposed method, it is compared with the GA.

• Korean Journal of Ecology and Environment
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• v.54 no.3
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• pp.170-189
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• 2021

Environmental DNA (eDNA) is a genetic material derived from organisms in various environments (water, soil, and air). eDNA has many advantages, such as high sensitivity, short investigation time, investigation safety, and accurate species identification. For this reason, it is used in various fields, such as biological monitoring and searching for harmful and endangered organisms. To collect eDNA from a freshwater ecosystem, it is necessary to consider the target organism and gene and a wide variety of items, such as on-site filtration and eDNA preservation methods. In particular, the method of collecting eDNA from the environment is directly related to the eDNA concentration, and when collecting eDNA using an appropriate collection method, accurate (good quality) analysis results can be obtained. In addition, in preserving and extracting eDNA collected from the freshwater ecosystem, when an accurate method is used, the concentration of eDNA distributed in the field can be accurately analyzed. Therefore, for researchers at the initial stage of eDNA research, the eDNA technology poses a difficult barrier to overcome. Thus, basic knowledge of eDNA surveys is necessary. In this study, we introduced sampling of eDNA and transport of sampled eDNA in aquatic ecosystems and extraction methods for eDNA in the laboratory. In addition, we introduced simpler and more efficient eDNA collection tools. On this basis, we hope that the eDNA technique could be more widely used to study aquatic ecosystems and help researchers who are starting to use the eDNA technique.

• Journal of the Korean Institute of Intelligent Systems
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• v.13 no.1
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• pp.37-44
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• 2003

In this paper, we investigated the performance of both DNA coding method and Genetic Algorithm(GA) in numeric pattern (from 0 to 9) recognition. The performance of the DNA coding method is compared to the that of the GA. GA searches effectively an optimal solution via the artificial evolution of individual group of binary string using binary coding, while DNA coding method uses four-type bases denoted by Adenine(A), Cytosine(C), Guanine(G) and Thymine(T). To compare the performance of both method, the same genetic operators(crossover and mutation) are applied and the probabilities of crossover and mutation are set the same values. The results show that the DNA coding method has better performance over GA. The reasons for this outstanding performance are multiple candidate solution presentation in one string and variable solution string length.

• Journal of KIISE:Computer Systems and Theory
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• v.36 no.4
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• pp.231-238
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• 2009

DNA sequences are the fundamental information for each species and a comparison between DNA sequences of different species is an important task. Since DNA sequences are very long and there exist many species, not only fast matching but also efficient storage is an important factor for DNA sequences. Thus, a fast string matching method suitable for encoded DNA sequences is needed. In this paper, we present a fast string matching method for encoded DNA sequences which does not decode DNA sequences while matching. We use four-characters-to-one-byte encoding and combine a suffix approach and a multi-pattern matching approach. Experimental results show that our method is about 5 times faster than AGREP and the fastest among known algorithms.

• Journal of Oral Medicine and Pain
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• v.20 no.2
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• pp.515-528
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• 1995

The human genomic deoxyribonucleic acid(DNA) was extracted from the pulp, dentin of 22 teeth by clelex, phenol methods. Samples of the tooth-derived DNA were amplified by polymerase chain reaction(PCR), electrophosed for sex determination by detection of X-Y homologus amelogenin gene and D1S80 locus detection The following results have been achieved. 1. Chelex and phenol method are effective to sex determination in the pulp and dentin 2. Chelex method is not suitable for detection of D1S80 locus. 3. Concentration and purity of DNA for teeth using chelex method is lower than using phenol method. From the above investigation, chelex method is simple, rapid for sex determination, but it is not suitable for detection of VNTRs.

• Korean Journal of Food Science and Technology
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• v.48 no.4
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• pp.335-340
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• 2016

This study was conducted to find out the most suitable DNA isolation methods for PCR detection of foodborne pathogens. Four DNA isolation methods including Universal Genomic DNA Extraction Kit (TaKaRa), PrepMan Ultra (Applied Biosystems), boiling method and alkaline lysis method (w/PEG) were tested and compared. The Universal Genomic DNA Extraction kit (TaKaRa) was considered as the more efficient isolation method for Escherichia coli O157:H7 and Staphylococcus aureus in lettuce, fish and beef. Meanwhile to detect the foodborne pathogens directly from foods without enrichment, the four different buffers such as double-distilled water, saline, glycine-saline, glycine-saline with Tween-20 and beef extract were also evaluated. As a result, saline was more suitable buffer for E. coli O157:H7. And double-distilled water was more suitable buffer than saline for S. aureus, respectively

• International Journal of Fuzzy Logic and Intelligent Systems
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• v.3 no.1
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• pp.121-126
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• 2003

In this paper, we propose a new wavelet-based fuzzy modeling using a DNA coding method. Generally, it is well known that the DNA coding method is more diverse in the knowledge expression and better in the optimization performance than the genetic algorithm (GA) because it can encode more plentiful genetic informations based on the biological DNA. The proposed method can construct a fuzzy model using the wavelet transform, in which the coefficients are identified by the DNA coding method. Thus, we can effectively get the fuzzy model of the nonlinear system by using the advantages of both wavelet transform and DNA coding method. In order to demonstrate the superiority of the proposed method, it is compared with modeling method using the conventional GA.

• Proceedings of the Korean Institute of Intelligent Systems Conference
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• 2001.12a
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• pp.225-228
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• 2001

DNA computing has been applied to the problem of getting an optimal solution since Adleman's experiment. DNA computing uses strings with various length and four-type bases that makes more useful for finding a global optimal solutions of the complex multi-modal problems. This paper presents DNA coding method for finding optimal solution of the multi-modal function and compares the efficiency of this method with the genetic algorithms (GA). GA searches effectively an optimal solution via the artificial evolution of individual group of binary string and DNA coding method uses a tool of calculation or Information store with DNA molecules and four-type bases denoted by the symbols of A(Ademine), C(Cytosine), G(Guanine) and T(Thymine). The same operators, selection, crossover, mutation, are applied to the both DNA coding algorithm and genetic algorithms. The results show that the DNA based algorithm performs better than GA.