• 미생물학회지
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• 제21권2호
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• pp.95-102
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• 1983

The penicillin G acylase(pga) gene was cloned in the vector plasmid pKM $300(Ar^r,\;Tc^r,\;6.33kb)$ for the study of the structure and expression of the pga gene. This recombinant plasmid pPAKS-1 DNA(24.5 Kb) was cleaved into 2 fragments by restriction enzyme Eco R1.1fragment by BamH1, 4fragments by Hind III, and 2 fragments by Pst I. The pga gene was located on the Eco R1.Hind III-C fragement of pPAKS-1. The recombinant plasmids pPAKS-1 and pPAKS-2, in which the Hind III-B and Hind III-D fragments pPAKS-1 are deleted, are characterized. The results are summarized as follows : 1. Doubling times of bacterial strain bearing pPAKS-1 and pPAKS-2 are 90 and 60 minutes, respectively. 2. pPAKS-1 and pPAKS-2 are present at about 16-32 and 70 copies per cell, respectively, are 0.66 and 5.5 units, respectively, which represent 2-fold and 20-fold higher enzyme 4. pPAKS-1 is very unstable, but pPAKS-2 is stable.

• BMB Reports
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• 제37권1호
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• pp.28-34
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• 2004

The discovery of biochemical and cellular functions of unannotated gene products begins with a database search of proteins with structure/sequence homologues based on known genes. Very recently, a number of frontier groups in structural biology proposed a new paradigm to predict biological functions of an unknown protein on the basis of its three-dimensional structure on a genomic scale. Structural proteomics (genomics), a research area for structure-based functional discovery, aims to complete the protein-folding universe of all gene products in a cell. It would lead us to a complete understanding of a living organism from protein structure. Two major complementary experimental techniques, X-ray crystallography and NMR spectroscopy, combined with recently developed high throughput methods have played a central role in structural proteomics research; however, an integration of these methodologies together with comparative modeling and electron microscopy would speed up the goal for completing a full dictionary of protein folding space in the near future.

• 미생물학회지
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• 제52권3호
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• pp.298-305
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• 2016

본 연구에서는 p-cresol 초기 분해에 관여하는 기존의 lap과 pcu 유전자군 외에 새로운 pch 유전자군을 Pseudomonas alkylphenolica KL28로 부터 동정하였다. 이 유전자군(pchACXF-pcaHG-orf4-pcaBC)은 p-cresol을 ${\beta}$-carboxy-cis,cis-muconate로의 전환을 촉매할 수 있는 효소를 암호화하는 것을 알 수 있었다. 이 유전자 군은 영국에서 분리된 Pseudomonas putida NCIMB 9866과 9869의 plasmid에서 유래된 pch 유전자 군과 동일하여, 이들 유전자군은 종간 horizontal gene transfer로 전달되었을 가능성을 제시하였다. 각 유전자군의 관련 유전자의 변이와 gfp 레포터를 갖는 프로모터의 발현 분석을 통해 3개의 분해 유전자군이 모두 p-cresol의 분해에 관여하는 것을 알 수 있었으며, pch 유전자는 p-cresol에 의해 유도되며, 고체 및 액체 배지에서도 pcu 유전자군이 가장 높게 발현되는 것을 확인할 수 있었다. 또한 pcu 유전자 변이주는 p-cresol을 이용하여 버섯모양의 공중체(aerial structure) 형성하지 않았으므로, 탄소원의 이용 속도가 다세포 구조 형성에 영향을 주는 중요한 요소 중의 하나임을 알 수 있었다.

• Genomics & Informatics
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• 제3권1호
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• pp.30-34
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• 2005

Microarray technology makes it possible to measure the expressions of tens of thousands of genes simultaneously under various experimental conditions. Identifying differentially expressed genes in each single experimental condition is one of the most common first steps in microarray gene expression data analysis. Reasonable choices of thresholds for determining differentially expressed genes are used for the next-stap-analysis with suitable statistical significances. We present a supervised model for identifying DEGs using pathway information based on the global connectivity structure. Pathway information can be regarded as a collection of biological knowledge, thus we are trying to determine the optimal threshold so that the consequential connectivity structure can be the most compatible with the existing pathway information. The significant feature of our model is that it uses established knowledge as a reference to determine the direction of analyzing microarray dataset. In the most of previous work, only intrinsic information in the miroarray is used for the identifying DEGs. We hope that our proposed method could contribute to construct biologically meaningful structure from microarray datasets.

• 한국양식학회:학술대회논문집
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• 한국양식학회 2003년도 추계학술발표대회 논문요약집
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• pp.42-42
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• 2003

The far eastern catfish (Silurus asotus) growth hormone (GH) gene was cloned and characterized. The complete nucleotide sequences of genomic GH gene sequences as well as a catfish GH cDNA were obtained by RT-PCR and gene filter screening. The GH cDNA and genomic gene span 1.0 and 1.8 kb from the start codon to the polyadenylation signal, respectively. Both on cDNA and gDNA GH genes, the sequence polymorphism was detected including various silence mutations. The genomic GH gene comprised of only four exons and three introns, which was novel type of fish GH gene structure. The evolutionary relation of the catfish GH gene was inferred based on the comparative phylogenic analysis using the gene structures and sequences.

• Journal of Microbiology
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• 제44권2호
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• pp.137-144
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• 2006

The problems associated with gene identification and the prediction of gene structure in DNA sequences have been the focus of increased attention over the past few years with the recent acquisition by large-scale sequencing projects of an immense amount of genome data. A variety of prediction programs have been developed in order to address these problems. This paper presents a review of the computational approaches and gene-finders used commonly for gene prediction in eukaryotic genomes. Two approaches, in general, have been adopted for this purpose: similarity-based and ab initio techniques. The information gleaned from these methods is then combined via a variety of algorithms, including Dynamic Programming (DP) or the Hidden Markov Model (HMM), and then used for gene prediction from the genomic sequences.

• 한국자원식물학회지
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• 제23권6호
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• pp.526-534
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• 2010

Genomes of clusters of related eukaryotes are now being sequenced at an increasing rate. In this paper, we developed an accurate, low-cost method for annotation of gene prediction and exon-intron structure. The gene prediction was adapted for delta 1-pyrroline-5-carboxylate-synthetase (p5cs) gene from China wild-type of the halophytic Leymus chinensis (Trin.), naturally adapted to highly-alkali soils. Due to complex adaptive mechanisms in halophytes, more attentions are being paid on the regulatory elements of stress adaptation in halophytes. P5CS encodes delta 1-pyrroline-5-carboxylate-synthetase, a key regulatory enzyme involved in the biosynthesis of proline, that has direct correlation with proline accumulation in vivo and positive relationship with stress tolerance. Using analysis of reverse transcription-polymerase chain reaction (RT-PCR) and PCR, and direct sequencing, 1076 base pairs (bp) of cDNA in length and 2396 bp of genomic DNA in length were obtained from direct sequencing results. Through gene prediction and exon-intron structure verification, the full-length of cDNA sequence was divided into eight parts, with seven parts of intron insertion. The average lengths of determinated coding regions and non-coding regions were 154.17 bp and 188.57 bp, respectively. Nearly all splice sites displayed GT as the donor sites at the 5' end of intron region, and 71.43% displayed AG as the acceptor sites at the 3' end of intron region. We conclude that this method is a cost-effective way for obtaining an experimentally verified genome annotation.

• The Plant Pathology Journal
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• 제29권3호
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• pp.234-241
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• 2013

Polygalacturonase (PG) gene is a typical gene family present in eukaryotes. Forty-nine PGs were mined from the genomes of Neurospora crassa and five Aspergillus species. The PGs were classified into 3 clades such as clade 1 for rhamno-PGs, clade 2 for exo-PGs and clade 3 for exo- and endo-PGs, which were further grouped into 13 sub-clades based on the polypeptide sequence similarity. In gene structure analysis, a total of 124 introns were present in 44 genes and five genes lacked introns to give an average of 2.5 introns per gene. Intron phase distribution was 64.5% for phase 0, 21.8% for phase 1, and 13.7% for phase 2, respectively. The introns varied in their sequences and their lengths ranged from 20 bp to 424 bp with an average of 65.9 bp, which is approximately half the size of introns in other fungal genes. There were 29 homologous intron blocks and 26 of those were sub-clade specific. Intron losses were counted in 18 introns in which no obvious phase preference for intron loss was observed. Eighteen introns were placed at novel positions, which is considerably higher than those of plant PGs. In an evolutionary sense both intron loss and gain must have taken place for shaping the current PGs in these fungi. Together with the small intron size, low conservation of homologous intron blocks and higher number of novel introns, PGs of fungal species seem to have recently undergone highly dynamic evolution.

• 한국잠사학회:학술대회논문집
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• 한국잠사학회 2003년도 International Symposium of Silkworm/Insect Biotechnology and Annual Meeting of Korea Society of Sericultural Science
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• pp.136-137
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• 2003

Fireflies, the luminescent insect, have species specific flash patterns, being recognized as sexual communication. The lucifrrase gene is sole enzyme responsible for bioluminescence. The firefly luciferase gene is widely used as a genetic marker or as a reporter gene in a variety of organism including bacteria, plants and animals. In this study, we illustrate the complete organization of the genomic structure of the luciferase gene from L. lateralis sampled in Boun and Muju, Korea. (omitted)

• Journal of Microbiology and Biotechnology
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• 제21권8호
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• pp.822-829
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• 2011

Evidence shows that probiotic bacteria can undergo substantial structural and morphological changes in response to environmental stresses, including antibiotics. Therefore, this study investigated the effects of penicillin G (0.015, 0.03, and 0.06 mg/l) on the morphology and adhesion of Lactobacillus acidophilus ATCC 4356, including the colony morphotype, biofilm production, hydrophobicity, $H_2_O2$ formation, S-layer structure, and slpA gene expression. Whereas only smooth colonies grew in the presence of penicillin, rough and smooth colony types were observed in the control group. L. acidophilus ATCC 4356 was found to be hydrophobic under normal conditions, yet its hydrophobicity decreased in the presence of the antibiotic. No biofilm was produced by the bacterium, despite testing a variety of different culture conditions; however, treatment with penicillin G (0.015-0.06 mg/l) significantly decreased its production of $H_2_O_2$ formation and altered the S-layer protein structure and slpA gene expression. The S-protein expression decreased with 0.015 mg/l penicillin G, yet increased with 0.03 and 0.06 mg/l penicillin G. In addition, the slpA gene expression decreased in the presence of 0.015 mg/l of the antibiotic. In conclusion, penicillin G was able to alter the S-layer protein production, slpA gene expression, and certain physicochemical properties of Lactobacillus acidophilus ATCC 4356.