• 한국축산식품학회지
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• 제37권6호
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• pp.884-888
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• 2017

In this study, we report the morphogenetic analysis and genome sequence of a new WCP30 phage of Weissella cibaria, isolated from a fermented food. Based on its morphology, as observed by transmission electron microscopy, WCP30 phage belongs to the family Siphoviridae. Genomic analysis of WCP30 phage showed that it had a 33,697-bp double-stranded DNA genome with 41.2% G+C content. Bioinformatics analysis of the genome revealed 35 open reading frames. A BLASTN search showed that WCP30 phage had low sequence similarity compared to other phages infecting lactic acid bacteria. This is the first report of the morphological features and complete genome sequence of WCP30 phage, which may be useful for controlling the fermentation of dairy foods.

• The Plant Pathology Journal
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• 제20권2호
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• pp.155-157
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• 2004

We isolated Rice dwarf virus (RDV) from infected plants in rice fields (Korea, Japan, China, the Philippines and Nepal) and analyzed their genomic dsRNAs by polyacrylamide gel eletrophoresis. The genomic dsRNAs of the isolates showed distinct electrophoretic mobility profiles. The S12 coding to nonstructural protein of Korean isolate (RDV-Kr) was further analyzed by sequencing. The S12 of RDV-Kr was 1,066bp long and coded for a protein composed of 312 amino acids including three open reading frames of P12, P120Pa and P120Pb. The sequence identities were 96% and 98.6% with Japanese isolates (H, AN), 94.7% with Nepalese isolate (NEL), 94% with Chinese isolate (CK) and the Philippines isolate (P).

• 한국식물병리학회지
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• 제12권4호
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• pp.389-394
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• 1996

도열병균, Magnaporthe grisea, 균주간의 유전적 유연관계를 분석하고 그들의 유전에 관한 '기본 정보를 얻고자 DNA polymorphism 분석을 실시하였다. 기주가 다른 도열병 균주들이 공시되었고 cloning에 의해 벼 도열병균 KJ201레이스 균주로부터 생성된 임의 선발 genomic clone들이 공시균주들간의 polymorphism을 밝히기 위해 사용되었던 바 그중 repectitive sequence를 보유한 repeated copy clone 하나가 선발되었다. Clone pMJ6에 의해 밝혀진 repetitive sequence는 Southern hybridization시 벼 분리균주에는 약 30개, 다른 기주 분리균에도 20∼33개의 밴드를 형성하였다. 반면 피 분리균주에는 단지 두 개의 밴드만을 나타내 분리기주가 다른 균주간에 뚜렷한 polymorphism이 존재하였으며 parsimony 분석에서도 역시 아주 먼 cluster를 형성하여 피 분리균은 다른 기주 분리균과 유전적으로 상당히 먼 것으로 추정되었다. 공시균의 genomic DNA를 HindIII로 처리했을 때 pMJ6에 의한 밴드양상은 공시균을 EcoRI으로 처리했을 때의 MGR probe의 밴드 양상과 유사하여 이 repeated copy clone이 도열병균주간의 유전적 유연관계를 분석하는데 MGR 못지않게 유용할 것으로 보인다.

• 한국미생물학회:학술대회논문집
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• 한국미생물학회 2002년도 추계학술대회
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• pp.180-182
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• 2002

Substantial genomic diversity has been expected among clinical isolates of H. pylori. We have suggested that the two complete H. pylori genomes already sequenced may be insufficient for providing a discriminatory tool for typing clinical isolates as well as an insight into the genomic diversity, which enable to establish strategy for control of H. pylori infection. In this study, we determine the nucleotide sequence of the entire genome of Korean strain 51 and compare it with two reported genomic sequences to suggest validity for extensive genomic sequencing of H. pylori. The genome of H. pylori 51 consists of a circular chromosome with a size of 1,591,297 bp, which is corresponding to $95.4\%\;and\;96.8\%$ of the 26695 and J99 chromosome length, respectively. We predict that there are 1,454 open reading frames (ORFs) in 51, representing $91.4\%\;and\;97.2\%$ of the reported numbers of ORF of 26695 and J99, respectively. In contrast to 26695 and J99 that have 123 and 65 strain-specific genes, respectively, of the 1,454 genes, only 39 genes are unique to 51. Differences in genomic organization between 51 and each foreign strain were greater than between 2 foreign strains in pair wise entire sequence alignments by BLASTN. Particularly, the extent of genomic rearrangement observed between 51 and 26695 is higher than between 51 and J99. Multiple sequence alignment of orthologous genes among 3 strains showed that 51 is genetically closer to 26695 rather than J99. Phylogenetic analysis of nonsynonymous and synonymous mutation indicated J99 has the longest branch length in the unrooted phylogenetic tree, suggesting that J99 has higher mutation rate than the other 2 strains.

• Journal of Plant Biotechnology
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• 제5권4호
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• pp.193-195
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• 2003

A major goal of agricultural biotechnology is the discovery of genes or genetic loci which are associated with characteristics beneficial to crop production. This knowledge of genetic loci may then be applied to improve crop breeding. Agriculturally important genes may also benefit crop production through transgenic technologies. Recent years have seen an application of high throughput technologies to agricultural biotechnology leading to the production of large amounts of genomic data. The challenge today is the effective structuring of this data to permit researchers to search, filter and importantly, make robust associations within a wide variety of datasets. At the Plant Biotechnology Centre, Primary Industries Research Victoria in Melbourne, Australia, we have developed a series of tools and computational pipelines to assist in the processing and structuring of genomic data to aid its application to agricultural biotechnology resear-ch. These tools include a sequence database, ASTRA, for the processing and annotation of expressed sequence tag data. Tools have also been developed for the discovery of simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) molecular markers from large sequence datasets. Application of these tools to Brassica research has assisted in the production of genetic and comparative physical maps as well as candidate gene discovery for a range of agronomically important traits.

• 대한바이러스학회지
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• 제28권4호
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• pp.327-335
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• 1998

Hantaan (HTN) and Seoul (SEO) viruses, murid rodent-borne hantaviruses, are known to causes hemorrhagic fever with renal syndrome (HFRS) in Korea. To determine the genomic diversity and molecular phylogeny of HTN and SEO viruses found in Korea, we amplified for part of M and S genomic segments of hantaviruses from sera of HFRS patients and lung tissues of hantavirus seropositive striped-field mice. Both M and S segment of 16 HTN and 2 SEO viruses were amplified by nested reverse transcription-polymerase chain reaction. Based on 324 nucleotides in the M genomic segment, the HTN and SEO strains showed $93.8{\sim}100%$ and $99.1{\sim}99.4%$ homologies, respectively. Similarly, based on 230 nucleotides in the S genomic segment, HTN and SEO strains showed $90.9{\sim}100%$ and 100% homologies, respectively. Phylogenetic analysis of M and S segments indicated that HTN strains could be divided into at least two main groups in M and S trees and the sequence differences detected among the Sand M genomic segments of HTN viruses are consistent with reassortment having taken place between HTN virus strains.

• 한국생물공학회:학술대회논문집
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• 한국생물공학회 2000년도 추계학술발표대회 및 bio-venture fair
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• pp.660-664
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• 2000

UK-58,852의 생합성에 관여하는 유전자를 분리하기 위해 Actinomadura roseorufa의 genomic DNA와 E. coli-Streptomyces shuttle cosmid vector인 pOJ446이 genomic library를 만들었다. Genomic library는 dehydratase PCR product와 eryA 유전자를 probe로 하여 sugar 생합성 유전자와 polyketide typel 유전자가 집단으로 존재하는 cosmid pHD54를 분리하였고, 이를 제한 효소인 BamHI, SmaI와 Sonicater를 이용해서 subcloning 하였다. 이들의 염기서열을 부분 분석한 결과, polyketide 생합성에 관여하는 ketoacyl synthase, methylmalonyl acyltransferase, ketoreductase, enolreductase 그리고 PKS loading domain 등 polyketide synthase type I 임을 보여주고 있고, BLAST 분석된 결과를 보면 polyketide synthase 유전자는 rifamycin 생합성 유전자와 유사성이 높다. 그리고 sugar 생합성에 관여하는 유전자로는 oxidoreductase, dTDP-D-glucose 4,6 dehydratase, dTDP-D-glucose synthase 그리고 dTDP-4-keto-6-deoxy-D-glycose 3,5-epimerase으로 구성된 gene cluster를 확인하였다. 그리고 염기서열 분석된 유전자중 dTDP-D-glucose synthase를 발현하여 유전자의 기능을 확인하였다.

• Asian-Australasian Journal of Animal Sciences
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• 제17권7호
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• pp.897-902
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• 2004

PSMC5 subunit, which belongs to the 26S proteasomal subunit family, plays an important role in the antigen presentation mediated by MHC class I molecular. Full-length cDNA of porcine PSMC5 was isolated using the in silico cloning and rapid amplification of cDNA ends (RACE). Amino acid was deduced and the primary structure was analyzed. Results revealed that the porcine PSMC5 gene shares the high degree of sequence similarity with its mammalian counterparts at both the nucleotide level and the amino acid level. The RT-PCR was performed to detect the porcine PSMC5 expression pattern in seven tissues and the result showed that high express level was observed in spleen, lung, marrow and liver while the low express level was in muscle. The full-length genomic DNA sequence of porcine PSMC5 gene was amplified by PCR and the genomic structure revealed that this gene was comprised by 12 exons and 11 introns. Best alignment of the cDNA and genomic exon DNA sequence presents 4 mismatches and this information potentially bears further study in gene polymorphisms.

• 한국생물정보학회:학술대회논문집
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• 한국생물정보시스템생물학회 2001년도 제2회 생물정보 워크샵 (DNA Chip Bioinformatics)
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• pp.61-86
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• 2001

All cancers are caused by abnormalities in DNA sequence. Throughout life, the DNA in human cells is exposed to mutagens and suffers mistakes in replication, resulting in progressive, subtle changes in the DNA sequence in each cell. Since the development of conventional and molecular cytogenetic methods to the analysis of chromosomal aberrations in cancers, more than 1,800 recurring chromosomal breakpoints have been identified. These breakpoints and regions of nonrandom copy number changes typically point to the location of genes involved in cancer initiation and progression. With the introduction of molecular cytogenetic methodologies based on fluorescence in situ hybridization (FISH), namely, comparative genomic hybridization (CGH) and multicolor FISH (m-FISH) in carcinomas become susceptible to analysis. Conventional CGH has been widely applied for the detection of genomic imbalances in tumor cells, and used normal metaphase chromosomes as targets for the mapping of copy number changes. However, this limits the mapping of such imbalances to the resolution limit of metaphase chromosomes (usually 10 to 20 Mb). Efforts to increase this resolution have led to the "new"concept of genomic DNA chip (1 to 2 Mb), whereby the chromosomal target is replaced with cloned DNA immobilized on such as glass slides. The resulting resolution then depends on the size of the immobilized DNA fragments. We have completed the first draft of its Korean Genome Project. The project proceeded by end sequencing inserts from a library of 96,768 bacterial artificial chromosomes (BACs) containing genomic DNA fragments from Korean ethnicity. The sequenced BAC ends were then compared to the Human Genome Project′s publicly available sequence database and aligned according to known cancer gene sequences. These BAC clones were biotinylated by nick translation, hybridized to cytogenetic preparations of metaphase cells, and detected with fluorescein-conjugated avidin. Only locations of unique or low-copy Portions of the clone are identified, because high-copy interspersed repetitive sequences in the probe were suppressed by the addition of unlabelled Cotl DNA. Banding patterns were produced using DAPI. By this means, every BAC fragment has been matched to its appropriate chromosomal location. We have placed 86 (156 BAC clones) cytogenetically defined landmarks to help with the characterization of known cancer genes. Microarray techniques would be applied in CGH by replacement of metaphase chromosome to arrayed BAC confirming in oncogene and tumor suppressor gene: and an array BAC clones from the collection is used to perform a genome-wide scan for segmental aneuploidy by array-CGH. Therefore, the genomic DNA chip (arrayed BAC) will be undoubtedly provide accurate diagnosis of deletions, duplication, insertions and rearrangements of genomic material related to various human phenotypes, including neoplasias. And our tumor markers based on genetic abnormalities of cancer would be identified and contribute to the screening of the stage of cancers and/or hereditary diseases

• Genomics & Informatics
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• 제14권3호
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• pp.70-77
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• 2016

Transposable elements are one of major sources to cause genomic instability through various mechanisms including de novo insertion, insertion-mediated genomic deletion, and recombination-associated genomic deletion. Among them is Alu element which is the most abundant element, composing ~10% of the human genome. The element emerged in the primate genome 65 million years ago and has since propagated successfully in the human and non-human primate genomes. Alu element is a non-autonomous retrotransposon and therefore retrotransposed using L1-enzyme machinery. The 'master gene' model has been generally accepted to explain Alu element amplification in primate genomes. According to the model, different subfamilies of Alu elements are created by mutations on the master gene and most Alu elements are amplified from the hyperactive master genes. Alu element is frequently involved in genomic rearrangements in the human genome due to its abundance and sequence identity between them. The genomic rearrangements caused by Alu elements could lead to genetic disorders such as hereditary disease, blood disorder, and neurological disorder. In fact, Alu elements are associated with approximately 0.1% of human genetic disorders. The first part of this review discusses mechanisms of Alu amplification and diversity among different Alu subfamilies. The second part discusses the particular role of Alu elements in generating genomic rearrangements as well as human genetic disorders.