• Fisheries and Aquatic Sciences
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• v.10 no.4
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• pp.179-185
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• 2007

Understanding dietary habits is one of the most important factors in studying food webs and other ecological processes. Here we designed universal primers to amplify portions of the 18S and 28S rDNA sequences to examine gut contents using PCR techniques. The gut contents of sailfin sandfish (Arctoscopus japonicus) and pacific squid (Todarodes pacificus) were examined. In total, 11 families of prey were identified with 18S and 28S rDNA using the universal primers. The DNA sequence data indicated that the primer sets successfully amplified a wide spectrum of species and represented gut contents in a relatively convenient way. We found that information in the NCBI database was not yet sufficient to discriminate the species we isolated. In addition, technology for the separation of heterogeneous PCR products and better resolution and quantification protocols would help increase data accuracy.

• 한국데이터정보과학회:학술대회논문집
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• 2006.04a
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• pp.121-129
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• 2006

Two color or cDNA microarrays are extensively used to study relative expression levels of thousands of genes simultaneously. 0かy two tissue samples can be hybridized on a single microarray slide. Thus, a microarray slide necessarily forms an incomplete block design with block size two when more than two tissue samples are under study. We also need to control for variability in gene expression values due to the two dyes. Thus, red and green dyes form the second blocking factor in addition to slides. General design problem for these microarray experiments is discussed in this paper. Designs for factorial cDNA microarrays are also discussed.

• Journal of the Institute of Electronics and Information Engineers
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• v.52 no.11
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• pp.66-78
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• 2015

With the development of bio computing technology, DNA watermarking to do as a medium of DNA information has been researched in the latest time. However, DNA information is very important in biologic function unlikely multimedia data. Therefore, the reversible DNA watermarking is required for the host DNA information to be perfectively recovered. This paper presents a reversible DNA watermarking using least square based prediction error expansion for noncodng DNA sequence. Our method has three features. The first thing is to encode the character string (A,T,C,G) of nucleotide bases in noncoding region to integer code values by grouping n nucleotide bases. The second thing is to expand the prediction error based on least square (LS) as much as the expandable bits. The last thing is to prevent the false start codon using the comparison searching of adjacent watermarked code values. Experimental results verified that our method has more high embedding capacity than conventional methods and mean prediction method and also makes the prevention of false start codon and the preservation of amino acids.

• Journal of Korea Multimedia Society
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• v.20 no.2
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• pp.244-253
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• 2017

Reversible DNA watermarking is capable of continuous DNA storage and forgery prevention, and has the advantage of being able to analyze biological mutation processes by external watermarking by iterative process of concealment and restoration. In this paper, we propose a reversible DNA watermarking method based on histogram multiple shifting of noncoding DNA sequence that can prevent false start codon, maintain original sequence length, maintain high watermark capacity without biologic mutation. The proposed method transforms the non-coding region DNA sequence to the n-th code coefficients and embeds the multiple bits of the n-th code coefficients by the non-recursive histogram multiple shifting method. The multi-bit embedding process prevents the false start codon generation through comparison search between adjacent concealed nucleotide sequences. From the experimental results, it was confirmed that the proposed method has higher watermark capacity of 0.004-0.382 bpn than the conventional method and has higher watermark capacity than the additional data. Also, it was confirmed that false start codon was not generated unlike the conventional method.

• Korean Journal of Ecology and Environment
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• v.54 no.3
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• pp.221-228
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• 2021

Recently, environmental DNA (eDNA)-based metabarcoding approaches have been proposed to evaluate the status of freshwater ecosystems owing to various advantages, including fast and easy sampling and minimal habitat disruption from sampling. Therefore, as a case study, we applied eDNA metabarcoding techniques to evaluate the effects of an abandoned mine land located near a headwater stream of Nakdonggang River, South Korea, by examining benthic macroinvertebrate diversity and compared the results with those obtained using the traditional Surber-net sampling method. The number of genera was higher in Surber-net sampling (29) than in the eDNA analysis (20). The genus richness tended to decrease from headwater to downstream in eDNA analysis, whereas richness tended to decrease at sites with acid-sulfated sediment areas using Surber-net sampling. Through cluster analysis and non-metric multidimensional scaling, the sampling sites were differentiated into two parts: acid-sulfated and other sites using Surber-net sampling, whereas they were grouped into the two lowest downstream and other sites using eDNA sampling. To evaluate freshwater ecosystems using eDNA analysis in practical applications, it is necessary to constantly upgrade the methodologies and compare the data with field survey methods.

• Korean Journal of Ecology and Environment
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• v.54 no.3
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• pp.151-155
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• 2021

The application of environmental DNA in the domestic ecosystem is also accelerating, but the processing and analysis of the produced data is limited, and doubts are raised about the reliability of the analyzed and produced biological taxa identification data, and the sample medium (target sample, water, air, sediment, Gastric contents, feces, etc.) and quantification and improvement of analysis methods are also needed. Therefore, in order to secure the reliability and accuracy of biodiversity research using the environmental DNA of the domestic ecosystem, it is a process of actively using the database accumulated through ecological taxonomy and undergoing verification procedures, and experts verifying the resolution of the data increased by gene sequence analysis. This is absolutely necessary. Environmental DNA research cannot be solved only by applying molecular biology technology, and interdisciplinary research cooperation such as ecology-taxa identification-genetics-informatics is important to secure the reliability of the produced data, and researchers dealing with various media can approach it together. It is an area in desperate need of an information sharing platform that can do this, and the speed of development will proceed rapidly, and the accumulated data is expected to grow as big data within a few years.

• Journal of Food Hygiene and Safety
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• v.35 no.6
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• pp.574-580
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• 2020

In this study we sought to determine the food fraud by discriminating species of commercial seafood product such as Larimichthys polyactis, Larimichthys crocea, Pennahia argentatus, and Miichthys miiuy, which are difficult to morphologically discriminate. After amplifying the mitochondrial cytochrome c oxidase subunit I gene of the reference fish, the DNA sequences of the amplified PCR products were analyzed. As a result, a 655 bp sequence for species identification was selected for use as DNA barcodes. To confirm the DNA data and primer set, the DNA barcode sequence of each fish was compared to that in that in the NCBI. All of the DNA barcode data were matched with the gene sequence of each fish in the NCBI. A total of 32 processed seafood products (8 L. polyactis, 12 L. crocea, 3 Pennahia argentatus, and 9 Miichthys miiuy) were investigated. Homology of 97% or more in DNA sequences was judged as the same species. As a result of the monitoring, there were no discovered cases of forgery or alteration. However, the use of a raw material name having no matching standard name in the Korea Food Code may cause consumer confusion. Therefore, it is suggested that the standard name or scientific name be co-labeled with the raw material name on seafood products to prevent consumer confusion.

• 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.

• Biomedical Science Letters
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• v.23 no.4
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• pp.372-379
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• 2017

This study was investigated to test whether paternal DNA that was destined for degradation was properly licensed by testing for the presence of mini-chromosome maintenance protein (MCM) 7 and origin recognition complex (ORC) 2 in the paternal pronuclei. ORC2 is one of the first licensing protein to come on and MCM7 is one of the last licensing protein to come on. Zygotes were prepared by injection of control and treated sperm injection (ICSI). To control for DNA breakage, epididymal spermatozoa were treated with DNase I to fragment the DNA, then injected into oocytes. The presence of MCM7 and ORC2 in the pronuclei of mouse zygotes was tested by immunohistochemistry, just before the onset of DNA synthesis, at 5 h after fertilization, and after DNA synthesis began, at 9 h post fertilization. We found that in all cases, both MCM7 and ORC2 were present in both pronuclei at 5 h after sperm injection, just before DNA synthesis began. This indicates that no matter how extensive the DNA damage, recruitment of licensing proteins to the origins of replication was not inhibited. Sperm DNA fragmentation does not prevent licensing of DNA replication origins. Furthermore, the embryo recognizes DNA that is damaged by nucleases. Our data indicate that the one-cell embryo does harbor a mechanism to prevent the replication of severely damaged DNA from spermatozoa, even though the embryos do not undergo classical apoptosis.

• Communications for Statistical Applications and Methods
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• v.11 no.1
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• pp.59-77
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• 2004

Since the introduction of DNA microarray, a revolutionary high through-put biological technology, a lot of papers have been published to deal with the analyses of the gene expression data from the microarray. In this paper we review most papers relevant to the cDNA microarray data, classify them in statistical methods' point of view, and present some statistical methods deserving consideration and future study.