• 한국컴퓨터정보학회논문지
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• 제14권5호
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• pp.29-36
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• 2009

서열데이터베이스에 있는 자주 발현하는 부분 서열을 패턴으로 찾아내는 순차패턴 탐색은 넓은 응용 분야를 가지는 중요한 데이터 마이닝 문제이다. DNA 서열에서 순차패턴이 모티프가 될 수 있으므로 DNA 서열에서 순차패턴을 찾는 것을 연구하였다. 대부분의 기존 마이닝 방법은 순차패턴의 정의에 따라 정확한 정합에 주력하여 노이즈가 있는 환경이나 실제 문제에서 발생하는 부정확한 데이터에 대하여 제대로 작동하지 않을 수 있다. 이러한 문제가 생물 데이터인 DNA 서열에서 자주 나타난다. 이러한 문제를 다루기 위한 근사 정합 방법을 연구하였다. 본 연구의 아이디어는 자주 발생하는 패턴을 근사 패턴이라 부르는 그룹으로 분류할 수 있다는 관찰에서 기반을 둔다. 기존의 Prefixspan 알고리즘은 주어진 긴 서열에서 순차패턴을 잘 찾을 수 있다. 본 연구는 Prefixspan 알고리즘을 개선하여 유사한 순차패턴을 찾을 수 있게 하였다. 실험 결과는 PreFixSpan보다 제안한 방법이 패턴 길이가 4일 때, 근사 순차패턴의 빈도가 5배 높아짐을 보였다.

• Journal of Animal Science and Technology
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• 제65권3호
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• pp.511-518
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• 2023

This study examined the association between functional sequence variants (FSVs) of myosin heavy chain 3 (MYH3) genotypes and collagen content in a Landrace and Jeju native pig (JNP) crossbred population. Four muscles (Musculus longissimus dorsi, Musculus semimembranosus, Musculus triceps brachii, and Musculus biceps femoris) were used for the analysis of meat collagen content, and the same animals were genotyped for the FSVs of the MYH3 gene by using PCR-RFLP (polymerase chain reaction-restriction fragment length polymorphism). Three FSVs of MYH3 genotypes were identified and had genotype frequencies of 0.358, 0.551, and 0.091 for QQ, Qq, and qq, respectively. QQ animals for the FSVs of the MYH3 genotypes showed higher collagen content in their M. longissimus dorsi (p < 0.001), M. semimembranosus (p < 0.001), M. triceps brachii (p < 0.001), and M. biceps femoris (p < 0.001) than qq homozygous animals. After the validation of this result in other independent populations, the FSVs of MYH3 genotypes can be a valuable genetic marker for improving collagen content in porcine muscles and can also be applied to increase the amount of collagen for biomedical purposes.

• Plant Breeding and Biotechnology
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• 제2권3호
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• pp.224-230
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• 2014

Amplified fragment length polymorphism (AFLP) is a molecular marker technique based on DNA and is extremely useful in detection of high polymorphism between closely related genotypes like Korean wheat cultivars. Six sequence characterized amplified regions (SCARs) have been developed from inter simple sequence repeat (ISSR) analysis which enabled the identification and differentiation of 13 Korean wheat cultivars from the other cultivars. We used six combinations of primer sets in our AFLP analysis for developing additional cultivar-specific markers in Korean wheat. Fifty-eight of the AFLP bands were isolated from EA-ACG/MA-CAC, EA-AGC/MA-CTG and EA-AGG/MA-CTA primer combinations. Of which 40 bands were selected to design SCAR primer pairs for Korean wheat cultivar identification. Three of 58 amplified primer pairs, KWSM006, KWSM007 and JkSP, enabled wheat cultivar identification. Consequently, 23 of 32 Korean wheat cultivars were classified by eight SCAR marker sets.

• 한국작물학회:학술대회논문집
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• 한국작물학회 2022년도 추계학술대회
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• pp.33-33
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• 2022

Rice (Oryza sativa L.) is a widely studied domesticated model plant. Seed awning is an unfavorable trait during rice harvesting and processing. Hence, awn was one of the target characters selected during domestication. However, the genetic mechanisms underlying awn development in rice are not well understood. In this study, we analyzed the genes for awn development using a mapping population derived from a cross between the Korean indica cultivar 'Milyang23' and NIL4/9 (derived from a cross between 'Hwaseong' and O. minuta). Two quantitative trait loci (QTLs), qAwn4 and qAwn9 were mapped on chromosome 4 and 9, respectively, increased awn length in an additive manner. Through comparative sequencing analyses parental lines, LABA1 was determined as the causal gene underlying qAwn4. qAwn9 was mapped to a 199-kb physical region between markers RM24663 and RM24679. Within this interval, 27 annotated genes were identified, and five genes, including a basic leucine zipper transcription factor 76 (OsbZIP76), were considered candidate genes for qAwn9 based on their functional annotations and sequence variations. Haplotype analysis using the candidate genes revealed tropical japonica specific sequence variants in the qAwn9 region, which partly explains the non-detection of qAwn9 in previous studies that used progenies from interspecific crosses. This provides further evidence that OsbZIP76 is possibly a causal gene for qAwn9. The O. minuta qAwn9 allele was identified as a major QTL associated with awn development in rice, providing an important molecular target for basic genetic research and domestication studies. Our results lay the foundation for further cloning of the awn gene underlying qAwn9.

• Molecules and Cells
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• 제46권11호
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• pp.700-709
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• 2023

Mucus hyperproduction and hypersecretion are observed often in respiratory diseases. MUC8 is a glycoprotein synthesized by epithelial cells and generally expressed in the respiratory track. However, the physiological mechanism by which extracellular nucleotides induce MUC8 gene expression in human airway epithelial cells is unclear. Here, we show that UTP could induce MUC8 gene expression through P2Y2-PLCβ3-Ca²⁺ activation. Because the full-length cDNA sequence of MUC8 has not been identified, a specific siRNA-MUC8 was designed based on the partial cDNA sequence of MUC8. siRNA-MUC8 significantly increased TNF-α production and decreased IL-1Ra production, suggesting that MUC8 may downregulate UTP/P2Y2-induced airway inflammation. Interestingly, the PDZ peptide of ZO-1 protein strongly abolished UTP-induced TNF-α production and increased IL-1Ra production and MUC8 gene expression. In addition, the PDZ peptide dramatically increased the levels of UTP-induced ZO proteins and TEER (trans-epithelial electrical resistance). These results show that the anti-inflammatory mucin MUC8 may contribute to homeostasis, and the PDZ peptide can be a novel therapeutic candidate for UTP-induced airway inflammation.

• 한국어병학회지
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• 제37권1호
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• pp.25-36
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• 2024

In this study, we analyzed the phylogenetic classification, epitope prediction, and pathogenicity of red sea bream iridovirus (RSIV) isolated from rock bream between 2019 and 2023. Phylogenetics based on genes encoding MCP and ATPase indicated that all five RSIV isolates belonged to RSIV subtype II. The deduced amino acid sequence of the MCP for the amplicons (1362 bp) obtained from RSIV isolates had a length of 453 amino acids. Among these, the amino acid sequences of the RSIV-19, 21, 22, and 23 isolates showed 100% identity, while the RSIV-20 isolate showed 99.78% identity with one residue difference at position 306. As a result of antigenicity analysis based on amino acid sequence, the antigenicity score of the RSIV-20 isolate was 0.6386 and the other RSIV isolates were 0.6365. Additionally, the prediction of their antigenic determinants resulted in a total of 17 identical antigenic plots. When each RSIV was inoculated into rock bream, no significant differences were observed with 100% cumulative mortality in all groups. This study provides data on the potential for genetic variation of RSIV isolated in the same marine area over the past five years, and the antigenicity and pathogenicity results of each isolate are expected to be useful information for selecting future vaccine strains.

• 식물분류학회지
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• 제34권1호
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• pp.43-61
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• 2004

한국산 제비꽃속 32분류군과 일본산 2집단 등 총 34집단에 대한 유연관계를 알아보기 위하여 RAPD(randomly amplified polymorphic DNA), ISSR(inter simple sequence repeat) 및 PCR-RFLP(restriction fragment length polymorphism) 분석을 실시하였다. RAPD 분석에서는 40개의 primer 중 6개가 분류군 전체에서 반응을 보였고 이로부터 총 70개(98.6%)의 다형화 밴드를 얻었으며, ISSR 분석에서는 4개의 primer로 부터 28개(96.6%)의 다형화밴드를 얻었다. 엽록체 DNA의 non-coding부분을 이용한 PCR-RFLP 분석에서는 반응이 일어난 4지역에서 증폭된 약 6.78 kb의 DNA 각각에 대하여 15가지 제한효소를 처리한 결과 총 80개의 restriction site를 얻었으며 그중 16 site는 polymorphic하게 나타나 20%의 다형화를 보였다. 본 연구에서 다룬 3가지 형질에 의한 유집분석 결과 각각의 형질에 의해서는 서로 일치하지 않는 유집형태를 보였지만 3가지 형질을 통합한 결과는 진정제비꽃절(sect. Nomimium)내 아절과 계열간 구분이 명확하게 나타났으며 무경종과 유경종도 구별이 가능하여 외부형태형질에 의한 기존의 분류체계와 일치하였다. 그러나 노랑제비꽃절(sect. Chamaemelanium)은 진정제비꽃절과 독립적인 군을 형성하지 않고 진정제비꽃절 내 무경종그룹인 Patellares아절과 Vaginatae아절 사이에 위치하여 나타났다. 형태적인 변이가 매우 심한 분류군으로 알려진 태백제비꽃군(V. albida complex)은 Patellares아절 내에서 하나의 군으로 유집되어 Pinnatae계열로 처리하는 것이 타당할 것으로 생각된다. 본 연구에서 사용한 3가지 형질 중 RAPD 분석방법은 ISSR과 PCR-RFLP 분석보다 제비꽃속의 종간 유연관계를 밝히는데 더 유용한 것으로 판단된다.

• 한국어병학회지
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• 제28권2호
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• pp.79-85
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• 2015

동해안에서 어획된 청자갈치 (Bothrocara hollandi)의 체측 근육에 유백색의 불투명한 시스트를 형성하고 있는 점액포자충이 발견되었다. 시스트를 마쇄하여 광학현미경으로 관찰해본 결과, 원형에 가까운 점액포자충의 성숙 포자가 관찰되었다. 성숙 포자의 평균 길이는 $11.9(11.0{\sim}13.5){\mu}m$, 평균 폭은 $11.6(10.7{\sim}13.6){\mu}m$, 평균 두께는 $7.8(6.9{\sim}8.8){\mu}m$이었다. 극낭의 평균 길이는 $4.4(3.2{\sim}5.3){\mu}m$이었으며, 평균 폭은 평균 $3.3(2.4{\sim}4.2){\mu}m$이었다. 감염숙주와 성숙포자의 형태학적 특징, 각 부위의 측정값으로부터 본 연구에서 발견된 점액포자충은 Myxobolus aeglefini Auerbach 1906으로 동정하였다. 또한 18S rDNA sequences를 이용한 계통분석 결과 M. albi와 M. groenlandicus와 같은 분지에 속하는 것이 확인되었으며 각각 97.7%와 96.9%의 상동성을 나타내었다.

• BMB Reports
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• 제38권6호
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• pp.739-747
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• 2005

Full-length cDNA sequences of four novel SPATA4 genes in chimpanzee, cow, chicken and ascidian were identified by bioinformatic analysis using mouse or human SPATA4 cDNA fragment as electronic probe. All these genes have 6 exons and have similar protein molecular weight and do not localize in sex chromosome. The mouse SPATA4 sequence is identified as significantly changed in cryptorchidism, which shares no significant homology with any known protein in swissprot databases except for the homologous genes in various vertebrates. Our searching results showed that all SPATA4 proteins have a putative conserved domain DUF1042. The percentages of putative SPATA4 protein sequence identity ranging from 30% to 99%. The high similarity was also found in 1 kb promoter regions of human, mouse and rat SPATA4 gene. The similarities of the sequences upstream of SPATA4 promoter also have a high proportion. The results of searching SymAtlas (http://symatlas.gnf.org/SymAtlas/) showed that human SPATA4 has a high expression in testis, especially in testis interstitial, leydig cell, seminiferous tubule and germ cell. Mouse SPATA4 was observed exclusively in adult mouse testis and almost no signal was detected in other tissues. The pI values of the protein are negative, ranging from 9.44 to 10.15. The subcellular location of the protein is usually in the nucleus. And the signal peptide possibilities for SPATA4 are always zero. Using the SNPs data in NCBI, we found 33 SNPs in human SPATA4 gene genomic DNA region, with the distribution of 29 SNPs in the introns. CpG island searching gives the data about CpG island, which shows that the regions of the CpG island have a high similarity with each other, though the length of the CpG island is different from each other.This research is a fundamental work in the fields of the bioinformational analysis, and also put forward a new way for the bioinformatic analysis of other genes.

• BMB Reports
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• 제39권4호
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• pp.346-354
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• 2006

The full-length cDNA of grass carp (Ctenopharyngodon idellus) and silver carp (Hypophthalmichthys molitrix) uncoupling protein 2 (UCP2) was obtained from liver. The grass carp UCP2 cDNA was determined to be 1152 bp in length with an open reading frame that encodes 310 amino acids. Five introns (Intron 3, 4, 5, 6 and 7) in the translated region, and partial sequence of Intron 2 in the untranslated region of grass carp UCP2 gene were also obtained. Gene structure comparison between grass carp and mammalian (human and mouse) UCP2 gene shows that, the UCP2 gene structure of grass carp is much similar to that of human and mouse. Partial UCP2 cDNA sequences of bighead carp (Aristichthys nobilis) and mud carp (Cirrhinus molitorella), were further determined. Together with the common carp (Cyprinus carpio) UCP2 sequence from GenBank (AJ243486), multiple alignment result shows that the nucleotide and amino acid sequences of the UCP2 gene, were highly conserved among the five major Chinese carps that belong to four subfamilies. Using beta-actin as control, the ratio UCP2/beta-actin mRNA (%) was determined to be $149.4{\pm}15.6$ (common carp), $127.4{\pm}22.1$ (mud carp), $96.7{\pm}12.7$ (silver carp), $94.1{\pm}26.8$ (bighead carp) and $63.7{\pm}16.2$ (grass carp). The relative liver UCP2 expression of the five major Chinese carps, shows a close relationship with their food habit: benthos and detrituseating fish (common carp and mud carp) > planktivorious fish (silver carp and bighead carp) > herbivorious fish (grass carp). We suggest that liver UCP2 might be important for Chinese carps to detoxify cyanotoxins and bacteria in debris and plankton food.