• Biomedical Science Letters
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• v.6 no.1
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• pp.1-9
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• 2000

To identity the genes responsible for the biosynthesis of exopolysaccharide, recombinant plasmids pUEX10 and pLEX10 were constructed from plasmid pLEX3 which was isolated from the recombinant cosmid library of Zoogloea ramigera 115. The complete nucleotide sequence of the 1.7 kb genomic DNA insert in plasmid pUEX10 was determined. Its analysis identified two open reading frames (ORF3 & ORF4) which could encode two proteins. The amino acid sequence derived from ORF3 showed the homology with gumC protein in Xanthomonas campestris as well as exoP protein in Rhizobium melizoti. The partial amino acid sequence of ORF4 showed the homology with polysaccharide export protein in Thermotoga maritima. Z. ramigera 115SLR and Z. ramigera 115SLR/pLEX10 showed the similar pattern for EPS production. Yield of exopolysaccharides produced by Z. ramigera 115SLR and Z. ramigera 115SLR/pLEX10 was 0.26% (w/v) and 0.16% (w/v), respectively.

• Journal of Plant Biotechnology
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• v.37 no.1
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• pp.89-95
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• 2010

Dihydroflavonol 4-reductase (DFR) is a key enzyme of the flavonoid biosynthesis pathway which catalyses the NADPH-dependent reduction of 2R,3R-trans-dihydroflavonols to leucoanthocyanidins. In this study we describe cloning and expression of the genes encoding the flavonoid-biosynthetic enzyme DFR in Gypsophila paniculata L. Inspection of the 1279 bp long sequence revealed an open reading frame 1063 bp, including a 36 bp 5' leader region and 181 bp 3' untranslated region. Comparison of the coding region of this DFR cDNA sequence including the sequences of Arabidopsis thaliana, Citrus sinensis, Dianthus caryophyllus, Ipomoea batatas, Matthiola incana, Nierembergia sp, Petunia hybrida, Solanum tuberosum, Vitis vinifera reveals an identity higher than 69% at the nucleotide level. The function of this nucleotide sequences was verified by comparison with amino acid sequences of the amino-terminus and tryptic peptides from purified plant enzyme, by northern blotting with mRNA from wild type and mutant plants, by in vitro expression yielding and enzymatically active reductase, as indicated by the small leucopelargonidin peak. Genomic southern blot analysis showed the presence of only one gene for DFR in Gypsophila paniculata.

• Korean Journal of Ichthyology
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• v.18 no.1
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• pp.12-19
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• 2006

To examine the relationship of geological distribution and phylogenetic tree of O. latipes in the Far East, we analyzed cytochrome b (cyt b) gene in the mitochondrial genome. In this study we employed the entire sequence of cyt b of 53 samples collected from nine Korean locations and 117 cyt b data retrieved from the GenBank. From 170 Oryzias latipes cyt b sequence data, 142 different haplotypes were identified and phylogenetic relationship was reconstructed based on the dataset. According to the phylogeny, haplotypes were divided into three major haplogroups A, B and C, and their relationships were well correlated to their distributional patterns. Haplogroup A which is widely distribute in the southern part of Korea is separated in the geographical distribution from the haplogroup B which is found from China to the western part of Korea. Haplogroup C is only found in Japan.

• Journal of the Institute of Electronics and Information Engineers
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• v.53 no.12
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• pp.67-75
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• 2016

DNA computing technology makes the interests on DNA storage and DNA watermarking / steganography that use the DNA information as a newly medium. DNA watermarking that embeds the external watermark into DNA information without the biological mutation needs the reversibility for the perfect recovery of host DNA, the continuous embedding and detecting processing, and the mutation analysis by the watermark. In this paper, we propose a reversible DNA watermarking based on circular histogram shifting of DNA code values with the prevention of false start codon, the preservation of DNA sequence length, and the high watermark capacity, and the blind detection. Our method has the following features. The first is to encode nucleotide bases of 4-character variable to integer code values by code order. It makes the signal processing of DNA sequence easy. The second is to embed the multiple bits of watermark into -order coded value by using circular histogram shifting. The third is to check the possibility of false start codon in the inter or intra code values. Experimental results verified the our method has higher watermark capacity 0.11~0.50 bpn than conventional methods and also the false start codon has not happened in our method.

• Korean Journal of Microbiology
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• v.40 no.2
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• pp.172-177
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• 2004

Photosynthetic bacteria, Rhodospirillum rubrum, have been reported to change their metabolic patterns depend-ing on the light condition. The genetic approach for such a metabolic change is one of main subject in pho-tosynthetic bacteria. It has been reported that the extrachromosomal plasmid might be related to this metabolic regulation. In this study, we have determined the partial sequences of R. rubrum plasmid pKYl with HindIII fragments and the predicted pKYl ORFs and physical map. We found the 8 putative proteins related to the genetic recombination of bacterium, which is reported to the alternative gene expression. Our results suggest that the genes located in pKYl are possibly involved in the metabolic switch according to the photocondition.

• Korean journal of applied entomology
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• v.55 no.3
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• pp.245-256
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• 2016

Elytra of Harmonia axyridis exhibit varied color patterns. In the present study, we deciphered the genetic basis for intraspecific diversity of elytra color patterns in H. axyridis, using amplified fragment length polymorphism (AFLP). Twenty-eight AFLP reactions were performed to generate a total of 2,741 bands. Of these, 20 bands were polymorphic for each color pattern. The polymorphic bands showed differences of genetic character among different color patterns of H. axyridis. Among them, ten candidate AFLP markers were color-linked. S1, S2, and S20 markers were detected in Succinea 1 and 2 variants of H. axyridis, whereas S3 and S5 were specifically detected in the Conspicua variant. S15, S18, and S19 were specific to the Succinea 2 variant. Polymerase chain reaction (PCR) products of these ten AFLP markers were sequenced. BLAST analysis of these sequences against the GenBank database revealed their homology to DNA fragments of unknown function. Based on the color-linked AFLP markers, sequence characterized amplified region (SCAR) markers were designed for PCR amplification of genomic DNA. Of the ten AFLP markers, five were successfully converted into SCAR markers, which could discriminate elytra color polymorphism in H. axyridis.

• Journal of KIISE:Databases
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• v.32 no.3
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• pp.263-275
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• 2005

In a large DNA database, indexing techniques are widely used for rapid approximate sequence searching. However, most indexing techniques require a space larger than original databases, and also suffer from difficulties in seamless integration with DBMS. In this paper, we suggest a space-efficient and disk-based indexing and query processing algorithm for approximate DNA sequence searching, specially exact match queries, wildcard match queries, and k-mismatch queries. Our indexing method places a sliding window at every possible location of a DNA sequence and extracts its signature by considering the occurrence frequency of each nucleotide. It then stores a set of signatures using a multi-dimensional index, such as R*-tree. Especially, by assigning a weight to each position of a window, it prevents signatures from being concentrated around a few spots in index space. Our query processing algorithm converts a query sequence into a multi-dimensional rectangle and searches the index for the signatures overlapped with the rectangle. The experiments with real biological data sets revealed that the proposed method is at least three times, twice, and several orders of magnitude faster than the suffix-tree-based method in exact match, wildcard match, and k- mismatch, respectively.

• Journal of Plant Biotechnology
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• v.33 no.2
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• pp.85-91
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• 2006

Flavanone 3$\beta$-hydroxylase (FHT) is an enzyme acting in the central part of the flavonoid biosynthesis pathway. FHT catalyses the hydroxylation of flavanone to dihydroflavonols in the anthocyanin pathway. In this paper we describe the cloning and expression of the genes encoding the flavonoid-biosynthetic enzyme FHT in Gypsophila paniculata L. A heterologous cDHA probe from Dianthus cavophyllus was used to isolate FHT-encoding cDHA clones from Gypsophila paniculata L.. Inspection of the 1471 bp long sequence revealed an open reading frame 1047 bp, including a 190 bp 5' leader region and 288 bp 3' untranslated region. Comparison of the coding region of this FHT cDHA sequence including the sequences of Arabidopsis thaliana, Citrus sinensis, Dianthus caryophyllus, Ipomoea batatas, Matthiola incana, Nierembergia sp, Petunia hybrida, Solanum tuberosum, Vitis vinifera reveals a identity higher than 69% at the nucleotide level. The function of this nucleotide sequences were verified by comparison with amino acid sequences of the amino-terminus and tryptic peptides from purified plant enzyme, by northern blotting with mRHA from wild type and mutant plants, by in vitro expression yielding and enzymatically active hydroxylase, as indicated by the small dihydrokaempferol peak. Genomic southern blot analysis showed the presence of only one gene for FHT in Gypsophila paniculata.

• Korean Journal of Food Science and Technology
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• v.50 no.5
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• pp.480-485
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• 2018

In this study, to identify single nucleotide polymorphisms (SNPs) associated with meat quality in Berkshire pigs, we performed RNA sequencing. A non-synonymous SNP (nsSNP) in the Complement component 9 (C9) gene was identified, and the association between meat quality traits and the C9 genotype was analyzed. The nsSNP in the C9 gene was located at c.942 G>T. In the dominant model, significant associations were observed between the SNP and meat quality traits such as CIE L, collagen content, moisture level, and $pH_{24h}$, whereas in the co-dominant model, significant associations were observed between the SNP and CIE L, collagen content, and protein content. In the recessive model, a significant association between the C9 genotype and the collagen content was observed. In addition, we identified the significant relationship between the C9 genotype and meat quality according to sex. These results indicate that the C9 SNP can be used as a genetic marker for improving pork quality.

• Journal of KIISE:Computer Systems and Theory
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• v.31 no.3_4
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• pp.145-151
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• 2004

We present an efficient data structure to obtain the range minima in an away in constant time. Recently, suffix ways are extensively used to search DNA sequences fast in bioinformatics. In constructing suffix arrays, solving the range minima problem is necessary When we construct suffix arrays, we should solve the range minima problem not only in a time-efficient way but also in a space-efficient way. The reason is that DNA sequences consist of millions or billions of bases. Until now, the most efficient data structure to find the range minima in an way in constant time is based on the method that converts the range minima problem in an array into the LCA (Lowest Common Ancestor) problem in a Cartesian tree and then converts the LCA problem into the range minima problem in a specific array. This data structure occupies O( n) space and is constructed in O(n) time. However since this data structure includes intermediate data structures required to convert the range minima problem in an array into other problems, it requires large space (=13n) and much time. Our data structure is based on the method that directly solves the range minima problem. Thus, our data structure requires small space (=5n) and less time in practice. As a matter of course, our data structure requires O(n) time and space theoretically.