• Applied Biological Chemistry
• /
• v.44 no.3
• /
• pp.153-161
• /
• 2001

In order to isolate genes involved in ecdysteroids biosynthesis in plants, total RNA was isolated from Achyranthes japonica Nakai, and RT-PCR was performed using degenerate primers selected based on the results of multi-alignment of four cytochrome P450 genes from plants and a putative ecdysone 20-hydroxylase gene from an insect. Fourteen partial cDNA clones showing unique base sequences were obtained, out of which six showed homologies at the levels of nucleotide and amino acid sequences to the other cytochrome P450 genes known to be involved in the ecdysteroid biosynthesis. Of the six clones, four showed relatively high homologies to a putative ecdysone 20-hydroxylase gene isolated from an insect.

• Proceedings of the Korean Information Science Society Conference
• /
• 2001.04b
• /
• pp.91-93
• /
• 2001

최근 지놈(Genome) 프로젝트를 통해 핵산, 단백질 서열 정보가 밝혀짐에 따라 분자 수준의 유전자 정보를 다루는 기법들이 활발히 연구되면서 방대한 서열 정보를 데이터 베이스화하고, 부족하기 위한 효과적인 도구와 컴퓨터 알고리즘의 개발을 필요로 하고 있다. 본 논문에서는 여러 단백질에 공통적으로 존재하는 서열 정보간에 존재하는 연관성을 탐사하기 위한 서열 연관 규칙 알고리즘을 제안한다. 원자 항목을 취급하였던 기존 알고리즘과는 달리 중복을 반영해야 하는 서열 데이터의 특성을 고려하여야 한다. 실험을 단백질 서열 데이터를 대상으로 수행하였다. 먼저 여러 서열에 빈발하게 발생하는 부 서열 집합을 찾고, 부 서열 집합들간에 존재하는 관련성을 탐사한다. 본 연구의 결과는 탐사된 규칙으로부터 다른 단백질의 구조와 기능을 예측할 수 있고, 이 정보는 필요로 하는 생물학적 분석을 방향을 제시할 것이다. 이는 생물학적 실험 대상의 후부조합을 최소화함으로써 많은 시간과 노력 비용을 절감할 수 있다.

• Journal of Ginseng Research
• /
• v.17 no.1
• /
• pp.69-76
• /
• 1993

• Korean Journal of Microbiology
• /
• v.40 no.2
• /
• pp.121-126
• /
• 2004

Comamonas sp. strain DJ-12 is a 4-chlobiphenyl(4CB)-degrading bacterium that was reidentified from Pseudomonas sp. DJ-12. The genomic DNA was isolated from the strain DJ-12 and amplified by PCR with primers for cloning pcbABCD genes responsible for degradation of 4CB. The amino acid sequences deduced from the nucleotide sequences of pcbA1, pcbA2, pcbA3, pcbA4, pcbB, pcbC2, and pcbD2 genes showed 91, 87, 99, 87, 97, 90 and 87％ homologies with those of Pseudomonas sp. KKS102, respectively. The pcbC1D1 genes that are involved in the degradation of (4-chloro)1,2-dihydroxybiphenyl produced from 4CB by pcbAB gene products were previously reported in the recombinant plasmid pCU1 from Pseudomonas sp. DJ-12. However, the pcbC2D2 genes in the plasmid pCT4 and pCT5 cloned from Comamonas sp. DJ-12 in this study showed 51 and 62％ homologies with those of pcbC1D1 in their nucleotide sequences. The pcbC1D1 and pcbC2D2 genes were found by Southern hybridization to be located at different loci on the chromosome of DJ-12 strain. These results indicate that Comamonas sp. strain DJ-12 has two different sets of pcbCD genes responsible for deg-radation of (4-chloro)1,2-dihydroxybiphenyl.

• Journal of Internet Computing and Services
• /
• v.5 no.5
• /
• pp.1-15
• /
• 2004

In this paper, we explain the design and implementation of GWB(Gene WorkBench), which is a web-based, integrated system for efficiently managing and analyzing genomic sequences, Most existing software systems handling genomic sequences rarely provide both managing facilities and analyzing facilities. The analysis programs also tend to be unit programs that include just single or some part of the required functions. Moreover, these programs are widely distributed over Internet and require different execution environments. As lots of manual and conversion works are required for using these programs together, many life science researchers suffer great inconveniences. in order to overcome the problems of existing systems and provide a more convenient one for helping genomic researches in effective ways, this paper integrates both managing facilities and analyzing facilities into a single system called GWB. Most important issues regarding the design of GWB are how to integrate many different analysis programs into a single software system, and how to provide data or databases of different formats required to run these programs. In order to address these issues, GWB integrates different analysis programs byusing common input/output interfaces called wrappers, suggests a common format of genomic sequence data, organizes local databases consisting of a relational database and an indexed sequential file, and provides facilities for converting data among several well-known different formats and exporting local databases into XML files.

• Journal of Animal Science and Technology
• /
• v.51 no.1
• /
• pp.1-8
• /
• 2009

We generated 57,598 expressed sequence tags (ESTs) from 3 cDNA libraries of Hanwooo (Korean Cattle), fat, loin, liver. Liver, intermuscular fat and longissimus dorsi tissues were obtained from a 24-month-old Hanwoo steer immediately after slaughter. cDNA library was constructed according to the oligocapped method. The EST data were clustered and assembled into unique sequences, 4,759 contigs and 7,587 singletons. To carry out functional analysis, Gene Ontology annotation and identification of significant leaf nodes were performed that were detected by searching significant p-values from $2^{nd}$ level GO terms to leaf nodes using Bonferroni correction. We found that 13, 26 and 8 significant leaf nodes are unique in the transcripts according to 3 GO categories, molecular function, biological process and cellular component. Also digital gene expression profiling using the Audic's test was performed and tissue specific genes were detected in the above 3 libraries.

• Korean Journal of Microbiology
• /
• v.35 no.1
• /
• pp.13-17
• /
• 1999

Shigella sonnez is important causes of human enleric infcctions. S. sonnei KNIH104S was isolated from patient of shigellosis in Korea and previously reported. We cloned 1.7 kb BamHI fragment containing the asd gene encoding an aspartate $\beta$-semialdehyde dehydrogenase from chromosomal DNA of S. sonnei KNIH104S. This recombinant plasmid was named as pSAB17. E. coli $\chi$6097, an a d mutant, cannol grow on the LB medium without DL-$\alpha$, $\varepsilon$-diaminopimclic acid (50 pgiml) but E. coli x 6097(pSAB17) can grow on the same medium. We sequenccd the asd gene ol Shigella for the first time. The asd gcne was composed of 1,104 base pairs with ATG initiation codon and TAA termination codon. Sequence comparison of the asd gene exhibited 99.9% nucleolide sequence hornology with that of E. coli. Also, We constructed the balanced-lethal vector using pBluescrip SK(+) and asd gene of S. sonnei KNIH104S.

• The Journal of the Korea Contents Association
• /
• v.22 no.2
• /
• pp.762-769
• /
• 2022

Genetic testing in prenatal diagnosis is a precious tool providing valuable information in clinical management and parental decision-making. For the last year, cytogenetic testing methods, such as G-banding karyotype analysis, fluorescent in situ hybridization, chromosomal microarray, and gene panels have evolved to become part of routine laboratory testing. However, the limitations of each of these methods demonstrate the need for a revolutionary technology that can alleviate the need for multiple technologies. The recent introduction of new genomic technologies based on next-generation sequencing has changed the current practice of prenatal testing. The promise of these innovations lies in the fast and cost-effective generation of genome-scale sequence data with exquisite resolution and accuracy for prenatal diagnosis. Here, we review the current state of sequencing-based pediatric diagnostics, associated challenges, as well as future prospects.

• Horticultural Science & Technology
• /
• v.29 no.2
• /
• pp.116-122
• /
• 2011

In this study, we report the generation and analysis of 1,392 expressed sequence tags (ESTs) from Korean Stewartia (Stewartia koreana Nakai). A cDNA library was generated from the young leaf tissue and a total of 1,392 cDNA were partially sequenced. EST and unigene sequence quality were determined by computational filtering, manual review, and BLAST analyses. Finally, 1,301 ESTs were acquired after the removal of the vector sequence and filtering over a minimum length 100 nucleotides. A total of 893 unigene, consisting of 150 contigs and 743 singletons, was identified after assembling. Also, we identified 95 new microsatellite-containing sequences from the unigenes and classified the structure according to their repeat unit. According to homology search with BLASTX against the NCBI database, 65% of ESTs were homologous with known function and 11.6% of ESTs were matched with putative or unknown function. The remaining 23.2% of ESTs showed no significant similarity to any protein sequences found in the public database. Annotation based searches against multiple databases including wine grape and populus sequences helped to identify putative functions of ESTs and unigenes. Gene ontology (GO) classification showed that the most abundant GO terms were transport, nucleotide binding, plastid, in terms biological process, molecular function and cellular component, respectively. The sequence data will be used to characterize potential roles of new genes in Stewartia and provided for the useful tools as a genetic resource.

• Journal of Animal Science and Technology
• /
• v.50 no.1
• /
• pp.9-18
• /
• 2008

Species-specific polymorphisms in chicken, pheasant, turkey, and quail were identified by cloning and sequencing of the immunoglobulin constant domain (IgLC). A set of species-specific primers were then designed on the basis of polymorphisms in the IgLC between species, as well as two additional sets of primers for the cytochrome b and tapasin genes, for the purpose of species identification. Together, the primers successfully distinguished specific species from chicken by species-specific PCR. This simple but unambiguous method may be used to screen avian inter-species germline chimeras, which are valuable models for the conservation of endangered species.