• The Journal of Korean Society of Virology
• /
• v.30 no.2
• /
• pp.101-112
• /
• 2000

Rotaviruses are the most common cause of severe vomiting and diarrhea in children worldwide and classified as a genus in the family Reoviridae. Rotavirus has eleven segmented dsRNAs and the virion consists of three shells. Outer capsid VP7 and VP4 induce neutralizing antibodies and are classified into G types (glycoprotein VP7) and P types (protease-sensitive VP4). Characterization of VP7 gene of Korean isolates of human rotavirus was performed using multiplex PCR and nucleotide sequence analysis. After RT-PCR amplification of full length (1,062 bp) of VP7 genes, the amplified PCR products were G typed by multiplex PCR and the nucleotide sequences were compared with those of reference rotavirus from GenBank. The G type analysis revealed that 25% (2/8) belong to G1, whereas 37.5% (3/8) benong to G2 and G4, respectively. The Korean isolates within the same serotypes showed high homology of nucleotide sequences and could be discriminated from foreign isolates exception with two strains (CAU009 and CAU022). But Korean isolates CAU009 and CAU022 were close related into japanease isolates 417 (99.2%) and indian isolates (97.6%) than Korean isolatese. Our results showed that these two strains were supposed to be originated from abroad. As a results, The G typing and nucleotide sequence analysis of VP7 gene of rotavirus isolated from infants in Korea could be used for identification, serotying and determination of novel or unusual strains of rotaviruses.

• The KIPS Transactions:PartD
• /
• v.16D no.5
• /
• pp.661-672
• /
• 2009

Recently it was found that various genetic structural variations such as CNV(copy number variation) exist in the human genome, and these variations are closely related with disease susceptibility, reaction to treatment, and genetic characteristics. In this paper we propose a new CNV detection algorithm using millions of short DNA sequences generated by giga-sequencing technology. Our method maps the DNA sequences onto the reference sequence, and obtains the occurrence frequency of each read in the reference sequence. And then it detects the statistically significant regions which are longer than 1Kbp as the candidate CNV regions by analyzing the distribution of the occurrence frequency. To select a proper read alignment method, several methods are employed in our algorithm, and the performances are compared. To verify the superiority of our approach, we performed extensive experiments. The result of simulation experiments (using a reference sequence, build 35 of NCBI) revealed that our approach successfully finds all the CNV regions that have various shapes and arbitrary length (small, intermediate, or large size).

• Journal of Plant Biotechnology
• /
• v.49 no.1
• /
• pp.30-38
• /
• 2022

Solanum brevicaule is one of the tuber-bearing wild Solanum species. Because of its resistance to several important pathogens infecting potatoes during cultivation, it can be used for potato breeding. However, the fact that S. brevicaule used in this study has an EBN value of two causes the sexual reproduction barriers between the species and cultivated potatoes. In this study, specific markers for discriminating S. brevicaule from other Solanum species were developed on the basis of the results of sequence alignments with the whole chloroplast genomes of S. brevicaule and seven other Solanum species. The chloroplast genome of S. brevicaule was completed by next-generation sequencing technology described in other recent studies. The total sequence length of the chloroplast genome of S. brevicaule is 155,531 bp. Its structure and gene composition are similar to those of other Solanum species. Phylogenetic analysis revealed that S. brevicaule was closely grouped with other Solanum species. BLASTN search showed that its genome sequence had 99.99% and 99.89% identity with those of S. spegazzinii (MH021562) and S. kurtzianum (MH021495), respectively. Sequence alignment identified 27 SNPs that were specific to S. brevicaule. Thus, three PCR-based CAPS markers specific to S. brevicaule were developed on the basis of these SNPs. This study will facilitate in further studies on evolutionary and breeding aspects in Solanum species.

• Animal Bioscience
• /
• v.36 no.10
• /
• pp.1517-1529
• /
• 2023

Objective: The objective of this study was to investigate the phylogenetic and expression analysis of the angiopoietin-like (ANGPTL) gene family and their role in lipid metabolism in pigs. Methods: In this study, the amino acid sequence analysis, phylogenetic analysis, and chromosome adjacent gene analysis were performed to identify the ANGPTL gene family in pigs. According to the body weight data from 60 Jinhua pigs, different tissues of 6 pigs with average body weight were used to determine the expression profile of ANGPTL1-8. The ileum, subcutaneous fat, and liver of 8 pigs with distinct fatness were selected to analyze the gene expression of ANGPTL3, ANGPTL4, and ANGPTL8. Results: The sequence length of ANGPTLs in pigs was between 1,186 and 1,991 bp, and the pig ANGPTL family members shared common features with human homologous genes, including the high similarity of the amino acid sequence and chromosome flanking genes. Amino acid sequence analysis showed that ANGPTL1-7 had a highly conserved domain except for ANGPTL8. Phylogenetic analysis showed that each ANGPTL homologous gene shared a common origin. Quantitative reverse-transcription polymerase chain reaction analysis showed that ANGPTL family members had different expression patterns in different tissues. ANGPTL3 and ANGPTL8 were mainly expressed in the liver, while ANGPTL4 was expressed in many other tissues, such as the intestine and subcutaneous fat. The expression levels of ANGPTL3 in the liver and ANGPTL4 in the liver, intestine and subcutaneous fat of Jinhua pigs with low propensity for adipogenesis were significantly higher than those of high propensity for adipogenesis. Conclusion: These results increase our knowledge about the biological role of the ANGPTL family in this important economic species, it will also help to better understand the role of ANGPTL3, ANGPTL4, and ANGPTL8 in lipid metabolism of pigs, and provide innovative ideas for developing strategies to improve meat quality of pigs.

• Fisheries and Aquatic Sciences
• /
• v.4 no.4
• /
• pp.192-196
• /
• 2001

Proopiomelanocortin (POMC) plays an essential role in the disease resistance system and is the precursor protein of biologically active peptides such as adrenocorticotropin (ACTH), $\alpha-melanocyte-stimulating$ hormone $(\alpha- MSH)$, $(\beta-melanocyte-stimulation hormone\;(\beta- MSH)$ and $\beta-endorphin$. We have isolated and sequenced two different forms of POMC cDNA, POMC-I and POMC-II, from a pituitary cDNA library of flounder. POMC-I cDNA consisted of 956 bp corresponding to deduced amino acids of 216 residues and POMC-II cDNA was 982 bp in length corresponding to 194 amino acids, respectively. The results of deduced amino acids analysis of the clones showed high sequence homology with previously reported POMCs amino acid sequences from various species. The homology between flounder POMC-I and -II is$57\%$ identity. We also constructed a phylogenetic tree based on POMC amino acid sequences.

• BMB Reports
• /
• v.42 no.9
• /
• pp.611-616
• /
• 2009

We investigated the expression pattern of dehydration responsive element-binding protein-3 in tomato under different abiotic stresses. Full length LeDREB3 cDNA was isolated from tomato plant, followed by phylogenetic analysis based on deduced amino acid sequences that revealed significant sequence similarity to DREB proteins belonging to diverse families of plant species. Southern blot analysis showed duplicate copies of LeDREB3 in the tomato genome while organ-specific expression profiling indicated constitutive expression of LeDREB3 in all tested organs, which was particularly strong in flower. LeDREB3 expression was significantly induced by Nacl, drought, low temperature and $H_2O_2$. Moreover, LeDREB3 was slightly regulated by treatment with ABA and MV. These observations suggest that the LeDREB3 gene may be involved in the response of the tomato plant to stress.

• Proceedings of the Korean Information Science Society Conference
• /
• 2004.10b
• /
• pp.304-306
• /
• 2004

생물정보학에서 서열의 유사성을 예측하는 것은 가장 중요한 문제 중의 하나이다. 염기 서열의 유사성을 검색하는 유용한 검색도구들에는 BLAST와 FASTA 등이 있으며 이러한 도구들은 새로운 유기체에 대한 실제 염기 서열을 필요로 한다. 이 경우 서열을 얻기 위한 sequencing 작업이 필요로 하며 시간적인 면에 있어서 상당한 비용을 요구한다. 본 논문에서는 sequencing 작업을 하지 않고 간단한 실험에서 얻을 수 있는 부분적인 Sequence 정보만을 대상으로 데이터 베이스에서 검색을 할 수 있는 두 개의 RIFLE(Rapid Identification of Microorganisms by Fragment Length Evaluation), MSMP(Maximum Site Matching Problem) 알고리즘을 구현하고 실험을 통해 두 알고리즘을 비교 평가한다. 실험결과 RIFLE 알고리즘이 수행 속도 면에서 빠른 반면 MSMP가 산출한 결과에 비해서 신뢰성이 떨어짐을 확인하였다.

• Structural Engineering and Mechanics
• /
• v.7 no.5
• /
• pp.473-484
• /
• 1999

In the present study, the thermal buckling analysis of thick anisotropic laminated composite plates is carried out using the finite strip method based on the higher-order shear deformation theory. This theory accounts for the parabolic distribution of the transverse shear strains through the thickness of the plate and for zero transverse shear stresses on the plate surfaces. Therefore, this theory yields improved results over the Mindlin plate theory and eliminates the need for shear correction factors in calculating the transverse shear stiffness. The critical temperatures of simply supported rectangular cross-ply and angle-ply composite laminates are calculated. The effects of several parameters, such as the aspect ratio, the length-to-thickness ratio, the number of plies, fibre orientation and stacking sequence, are investigated.

• Korean Journal of Child Studies
• /
• v.29 no.5
• /
• pp.1-12
• /
• 2008

This study investigated the development of complex sentences in the early utterances of Korean-Chinese children. The subjects were 47(20 2-year-old, 15 3-year-old, and 12 4-year-old) Korean-Chinese children living in China. Each child's spontaneous natural speech during interaction with his/her caregiver was videotaped for about 30 minutes and analyzed for Korean complex sentences using Kim's(2000) categories and Korean Computerized Language Analysis 2.0(2000). Results showed that older children were higher in Mean Length of Utterance and in number and frequency of word types than younger children. The language development of bilingual children was delayed compared with monolingual children but the developmental sequence between bilingual and monolingual children was similar.

• Journal of Institute of Control, Robotics and Systems
• /
• v.9 no.11
• /
• pp.943-951
• /
• 2003

A strategy for fault-tolerant gaits of autonomous legged robots is proposed. A legged robot is considered to be fault tolerant with respect to a given failure if it is guaranteed to be capable of walking maintaining its static stability after the occurrence of the failure. The failure concerned in this paper is a locked joint failure for which a joint in a leg cannot move and is locked in place. If a failed joint is locked, the workspace of the resulting leg is constrained, but legged robots have fault tolerance capability to continue static walking. An algorithm for generating fault-tolerant gaits is described and, especially, periodic gaits are presented for forward walking of a hexapod robot with a locked joint failure. The leg sequence and the formula of the stride length are analytically driven based on gait study and robot kinematics. The transition procedure from a normal gait to the proposed fault-tolerant gait is shown to demonstrate the applicability of the proposed scheme.