• Archives of Pharmacal Research
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• v.20 no.6
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• pp.550-554
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• 1997

Chlorambucil is known to alkylate primarily N7 of guanine and N3 of adenine to induce DNA monofunctional adducts and interstrand cross-links (ISC). We have investigated the sequence specificity for DNA ISC induced by chlorambucil using duplex oligomers containing a defined cross-linkable sequences $ 5^{I}-A*TT, 5^{I}-G*TTor5^{I}-G*CC$ under bar which asterisk indicates the potential cross-linking site and underlined base indicates the potential cross-linking site on the opposite strand. An analysis of 20% denaturing polyacrylamide gel electrophoresis showed that chlorambucil was albe to induce DNA ISC in the duplex oligomers containing a sequence $5^I-GCC$. The formation of DNA ISC was not observed in the duplex oligomers containing sequences $5^I-ATT$. or $5^I-GTT$. These results indicate that chlorambucil induces guanine-guanine DNA ISC but not guanine-adenine or adenine-adenine DNA ISC. In addition, we have tested the ability of chlorambucil to induce DNA ISC within $5^I-GNNC$ or $5^I-GNNC$sequences using duplex oligomers containing the sequence$5^I-G^4G^3G^2^C$. The result of DNA strand cleavage assay showed that DNA ISC was formed at the $5^I-GGC$ sequence (an 1,3 cross-link, $G^1-G^3$) but not at $5^I-GGGC$ (an 1,4 cross-link, $G^1-G^4$) or $5^I-GC$ sequence (an 1,2 cross-link, $G^1-G^2$).

• International journal of advanced smart convergence
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• v.5 no.3
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• pp.8-15
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• 2016

In recent years, one of deep learning models called Deep Belief Network (DBN) which formed by stacking restricted Boltzman machine in a greedy fashion has beed widely used for classification and recognition. With an ability to extracting features of high-level abstraction and deal with higher dimensional data structure, this model has ouperformed outstanding result on image and speech recognition. In this research, we assess the applicability of deep learning in dna classification level. Since the training phase of DBN is costly expensive, specially if deals with DNA sequence with thousand of variables, we introduce a new encoding method, using decimal-binary vector to represent the sequence as input to the model, thereafter compare with one-hot-vector encoding in two datasets. We evaluated our proposed model with different contrastive algorithms which achieved significant improvement for the training speed with comparable classification result. This result has shown a potential of using decimal-binary vector on DBN for DNA sequence to solve other sequence problem in bioinformatics.

• International Journal of Industrial Entomology and Biomaterials
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• v.4 no.2
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• pp.163-168
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• 2002

We report for the first time the cDNA sequence encoding a ferritin subunit from the spiders Araneus ventricosus. The complete cDNA sequence of A. ventricosus ferritin subunit comprised 516 bp with 172 amino acid residues. The A. ventricosus ferritin subunit cDNA contained a conserved iron responsive element sequence in the 5 untranslated region. An alignment of the deduced protein sequence of the A. ventricosus ferritin subunit gene to that of other heavy chain ferritin molecules showed that A. ventricosus ferritin subunit is most similar to the great pond snail, Lymnaea stagnalis, ferritin with 70.2% of protein sequence identity.

• Archives of Pharmacal Research
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• v.21 no.4
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• pp.385-390
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• 1998

Adozelesin and carzelesin are synthetic analogues of the extremely potent antitumor antibiotic CC-1065, which alkylates N3 of adenine in a consensus sequence $5^1$-(A/T)(A/T)$A^*$ ($A^*$ is the site of alkylation). We have investigated the DNA sequence selectivity of adozelesin and carzelesin by thermally ind ced DNA strand cleavage assay using radiolabeled restriction DNA fragments. An analysis of alkylation patterns shows that the consensus sequences for carzelesin and adozelesin have been found to be $5^1$-(A/T)(A/T)$A^*$ and $5^1$-(A/F)(G/C)(A/T)$A^*$. A new consensus sequence, $5^1$-(A/T)(A/T)$CA^*$, has been observed to display an additional alkylation site for adozelesin but not for carzelesin. These results indicate that the pattern of sequence selectivity induced by carzelesin is similar but not identical to those induced by adozelosin.

• Animal cells and systems
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• v.3 no.1
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• pp.69-72
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• 1999

A tandemly repeated DNA sequence was identified and characterized y the combined RAPD and FISH data from a total genomic DNA of Welsh onion (Allium fistulosum). A clone containing this repeating sequence was selected and sequenced. This repeating unit of 314 bp inserted into pAf 072 contained 54.1% adenine and thymine residues, and showed the primer sequence used, 5'-GAAACGGGTG-3', in both terminals of the sequence. Fluorescence in situ hybridization using this tandemly repeated sequence as a probe indicated that the detected sites were coincident with the major C-banded constitutive heterochromatin in the terminal regions of both arms of all 6 chromosomes.

• Journal of the Institute of Electronics and Information Engineers
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• v.51 no.10
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• pp.118-127
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• 2014

DNA data storage refers to any technique for storing massive digital data in base sequence of DNA and has been recognized as the future storage medium recently. This paper presents an information hiding method for DNA data storage that the massive data is hidden in non-coding strand based on DNA steganography. Our method maps the encrypted data to the data base sequence using the numerical mapping table and then hides it in the non-coding strand using the key that consists of the seed and sector length. Therefore, our method can preserve the protein, extract the hidden data without the knowledge of host DNA sequence, and detect the position of mutation error. Experimental results verify that our method has more high data capacity than conventional methods and also detects the positions of mutation errors by the parity bases.

• Journal of Life Science
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• v.14 no.6 s.67
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• pp.963-966
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• 2004

The sequence of ITS (partial 16S ribosomal DNA, complete ITS1, 5.8S ribosomal DNA and ITS2, and partial 28S ribosomal DNA) was analysed by PCR and autosequencing in Sarcodon aspratus. The ITS lenght of S. aspratus was 716 base pair. As this sequence compared with other reports on S. aspratus (ace No AF335110), the sequence variation based on nucleotide deletion and substitution was $1.8\%$. This nucleotide variation rate in same species was very higher than in other species. Also, the sequence varitation rates between this S. aspratus and S. imbricatus, and S. squamus were $8\%\;and\;10\%$, respectively. This results suggested that the high sequence variation of S. aspratus might be caused specific host and inhabitat environment which limited gene flow.

• Ocean Science Journal
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• v.40 no.3
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• pp.155-166
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• 2005

New PCR primers (N=18) were designed for the isolation of complete SSU to LSU rDNA sequences from the dinoflagellate Alexandrium tamarense. Standard PCR, employing each primer set selected for amplifications of less than 1.5 kb, successfully amplified the expected rDNA regions of A. tamarense (Korean isolate, HY970328M). Complete SSU, LSU rDNAs and ITS sequences, including 5.8S rDNA, were recorded at 1,800 bp, 520 bp and 3,393 bp, respectively. The LSU rDNA sequence was the first report in Alexandrium genus. No intron was found in the LSU rRNA coding region. Twelve D-domains within the LSU rDNA were put together into 1,879 bp (44.4% G+C), and cores into 1514 bp (42.8% G+C). The core sequence was significantly different (0.0867 of genetic distance, 91% sequence similarity) in comparison with Prorocentrum micans (GenBank access. no. X16108). The D2 region was the longest in length (300 bp) and highly variable among the 12 D-domains. In a phylogenetic analysis using complete LSU rDNA sequences of a variety of phytoplankton, A. tamarense was clearly separated with high resolution against other species. The result suggests that the sequence may resolve the taxonomic ambiguities of Alexandrium genus, particularly of the tamarensis complex.

• Journal of the Institute of Electronics and Information Engineers
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• v.52 no.7
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• pp.51-62
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• 2015

Of recent interests on high capacity DNA storage, DNA watermarking for DNA copyright protection, and DNA steganography for DNA secret communication are augmented, the reversible DNA watermarking is much needed both to embed the watermark without changing the functionality of organism and to perfectly recover the host DNA sequence. In this paper, we address two ways of DE based reversible DNA watermarking using noncoding DNA sequence. The reversible DNA watermarking should consider the string structure of a DNA sequence, the organism functionality, the perfect recovery, and the high embedding capacity. We convert the string sequence of four characters in noncoding region to the decimal coded values and embed the watermark bit into coded values by two ways; DE based multiple bits embedding (DE-MBE) using pairs of neighbor coded values and consecutive DE-MBE (C-DE-MBE). Two ways process the comparison searching to prevent the false start codon that produces false coding region. Experimental results verified that our ways have more high embedding capacity than conventional methods and produce no false start codon and recover perfectly the host sequence without the reference sequence. Especially C-DE-MBE can embed more high two times than DE-MBE.

• Journal of the Institute of Electronics and Information Engineers
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• v.49 no.10
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• pp.91-101
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• 2012

DNA watermarking have been interested for both the security of private genetic information or huge DNA storage information and the copyright protection of GMO. Multimedia watermarking has been mainly designed on the basis of frequency domain, such as DCT, DWT, FMT, and so on, for the robustness and invisibility. But a frequency domain watermarking for coding DNA sequence has a considerable constraint for embedding the watermark because transform and inverse transform must be performed without completely changing the amino acid sequence. This paper presents a coding sequence watermarking on lifting based DWT domain and brings up the availability of frequency domain watermarking for DNA sequence. From experimental results, we verified that the proposed scheme has the robustness to until a combination of 10% point mutations, 5% insertion and deletion mutations and also the amino preservation and the security.