• Interdisciplinary Bio Central
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• v.4 no.4
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• pp.14.1-14.6
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• 2012

Splice site prediction in DNA sequence is a basic search problem for finding exon/intron and intron/exon boundaries. Removing introns and then joining the exons together forms the mRNA sequence. These sequences are the input of the translation process. It is a necessary step in the central dogma of molecular biology. The main task of splice site prediction is to find out the exact GT and AG ended sequences. Then it identifies the true and false GT and AG ended sequences among those candidate sequences. In this paper, we survey research works on splice site prediction based on support vector machine (SVM). The basic difference between these research works is nucleotide encoding technique and SVM kernel selection. Some methods encode the DNA sequence in a sparse way whereas others encode in a probabilistic manner. The encoded sequences serve as input of SVM. The task of SVM is to classify them using its learning model. The accuracy of classification largely depends on the proper kernel selection for sequence data as well as a selection of kernel parameter. We observe each encoding technique and classify them according to their similarity. Then we discuss about kernel and their parameter selection. Our survey paper provides a basic understanding of encoding approaches and proper kernel selection of SVM for splice site prediction.

• Journal of Microbiology and Biotechnology
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• v.1 no.1
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• pp.17-21
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• 1991

A gene coding for ${\beta}-xylosidase$ in alkalophilic Bacillus sp. YC-335 isolated from soil was cloned into Escherichia coli HB101 using plasmid pBR322. The recombinant plasmid pYK40 was isolated, and the cloned HindIII fragment was 15 kilobases (kb). To reduce the size of the inserted DNA fragment of pYK40, the 15 kb HindIII fragment was subjected to a series of subclonings. A 6 kb subfragment was found to code for ${\beta}-xylosidase$ activity, and the recombinant plasmid was named pYK44. Southern hybridization analysis revealed that the cloned gene hybridized with 3.5 kb, 1.5 kb, and 1.0 kb of HindIII cleaved chromosomal DNA from Bacillus sp. YC-335. ${\beta}-xylosidase$ activity produced by recombinant E. coli was found to be 11 times higher than that produced by Bacillus sp. YC-335. Xylan was required to induce the production of ${\beta}-xylosidase$ in Bacillus sp. YC-335.

• Journal of Microbiology and Biotechnology
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• v.2 no.4
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• pp.237-242
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• 1992

In order to clone the gene coding for alkaline phosphatase in the yeast Kluyveromyces fragilis, a genomic library was constructed using the yeast-E. coli shuttle vector pHN114 as a cloning vector. From the genomic library, a clone carrying the gene was isolated and the plasmid was designated as pSKH101. A restriction enzyme map was made using this plasmid. Subcloning experiments and complementation studies showed that alkaline phosphatase was active only in the original 3.1 kb insert. Southern hybridization analysis confirmed that the cloned DNA fragment was derived from K. fragilis genomic DNA. Using a minicell experiment, the product of the cloned gene was identified as a protein with a molecular weight of 63 KDa. A 0.6 kb HindIII fragment, which showed promoter activity, was isolated using the E. coli promoter-probe vector pKO-1.

• Korean Journal of Microbiology
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• v.53 no.3
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• pp.216-218
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• 2017

We here provide the complete genome sequence of Bacillus thuringiensis C25, the strain showing antagonistic effects on fungal phytopathogens. The genome comprised of 5,308,062 bp with 35.32% G+C content of a circular chromosome and a plasmid containing 308,946 bp with 32.23% G+C content. The chromosome and plasmid genome included 5,683 protein coding DNA sequences, 107 tRNA and 42 rRNA genes.

• The Plant Pathology Journal
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• v.34 no.5
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• pp.445-450
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• 2018

Bacteriophages, bacteria-infecting viruses, have been recently reconsidered as a biological control tool for preventing bacterial pathogens. Erwinia amylovora and E. pyrifoliae cause fire blight and black shoot blight disease in apple and pear, respectively. In this study, the bacteriophage phiEaP-8 was isolated from apple orchard soil and could efficiently and specifically kill both E. amylovora and E. pyrifoliae. This bacteriophage belongs to the Podoviridae family. Whole genome analysis revealed that phiEaP-8 carries a 75,929 bp genomic DNA with 78 coding sequences and 5 tRNA genes. Genome comparison showed that phiEaP-8 has only 85% identity to known bacteriophages at the DNA level. PhiEaP-8 retained lytic activity up to $50^{\circ}C$, within a pH range from 5 to 10, and under 365 nm UV light. Based on these characteristics, the bacteriophage phiEaP-8 is novel and carries potential to control both E. amylovora and E. pyrifoliae in apple and pear.

• The Plant Pathology Journal
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• v.21 no.1
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• pp.13-20
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• 2005

Chlorella viruses are large icosahedral, plaque-forming, dsDNA viruses that infect certain unicellular, chlorellalike green algae. The genomic DNA of over 300 kb contains many useful genes and promoters. Over 40 chlorella viruses have been isolated from fresh water in Korea since 1998. The viruses were amplified initially in chlorella strain NC64A, and pure isolates were obtained by repeated plaque isolation. SDS-PAGE analysis revealed similar but distinct protein patterns, both among the group of purified viruses and in comparison with the prototype chlorella virus PBCV-1. Digestions of the 330- to 350-kb genomic DNAs with 10 restriction enzymes revealed different restriction fragment patterns among the isolates. The tRNA-coding regions of 8 chlorella viruses were cloned and sequenced. These viruses contain 14-16 tRNA genes within a 1.2- to 2-kb region, except for the SS-1 isolate, which has a 1039-bp spacer in a cluster of 11 tRNA genes. Promoter regions of several early genes were isolated and their activities were analyzed in transformed chlorella. Some promoters showed stronger activity than commonly used CaMV 35S promoter and chlorella transformation vectors for heterologous protein are beings constructed using these promoters.

• Journal of Forest and Environmental Science
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• v.30 no.3
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• pp.307-313
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• 2014

This study was conducted to distinguish the pines that are too similar to differentiate using conventional methods. Pinus densiflora and Pinus sylvestris have similar anatomical structure. They both have window-like pits and dentate ray tracheids, so it is not easy to distinguish the plants. We tried to find molecular markers by comparing chloroplast DNA sequences to differentiate the pines growing in Korea. We used P. densiflora, P. densiflora for. multicaulis, P. sylvestris, P. rigida, P. rigitaeda, P. koraiensis, and P. bungeana for this study. We found that the non-coding intergenic region of trnT(UGU) and trnL(UAA) genes have differences among the species. We designed a primer set to amplify the region efficiently and compared the PCR product sequences using CLC Workbench programs to find the polymorphism. We could distinguish the species using the sequences of the amplified region and the sequences were reproducible from the pines collected in Korea.

• BMB Reports
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• v.34 no.6
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• pp.502-508
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• 2001

A cDNA, encoding the human growth hormone (hGH), was synthesized based on the known 191 amino acid sequence. Its codon usage was optimized for a high level expression in Escherichia coli. Unique restriction sites were incorporated throughout the gene to facilitate mutagenesis in further studies. To minimize an initiation translation problem, a 624-bp cassette that contained a ribosome binding site and a start codon were fused to the hGH-coding sequence that was flanked between the EcoRI and HindIII sites. The whole fragment was synthesized by an overlapped extension of eight long synthetic oligonucleotides. The four-short duplexes of DNA, which were first formed by annealing and filling-in with a Klenow fragment, were assembled to form a complete hGH gene. The hGH was cloned and expressed successfully using a pET17b plasmid that contained the T7 promoter. Recombinant hGH yielded as much as 20% of the total cellular proteins. However, the majority of the protein was in the form of insoluble inclusion bodies. N-terminal amino acid sequencing also showed that the hGH produced in E. coli contained formyl-methionine. This study provides a useful model for synthesis of the gene of interest and production of recombinant proteins in E. coli.

• Journal of Microbiology
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• v.34 no.2
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• pp.151-157
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• 1996

By PCR amplification using the sequence of the previously cloned shiga-like toxin II DNA, a gene encoding it has been cloned from an isolate of healthy Korean native bovine feces, Escherichia coli KSC109. The nucleotide sequence s included tow open reading frames coding for 319 and 89 amino acids corresponding to A and B subunits, respectively. Comparison of the nucleotide and predicted amino acid sequences of newly cloned gene (slt-II) with those of others in the SLT-II family revealed completely identical homology with SLT-II cloned previously from bacteriophabe DNA of E. coli 933 derived from a patient with hemorrhagic colities. In addition, the sequence homology of SLT-II with SLT-II variant form bovine was more than 95% at both the nucleotide and protein levels. Overexpression of SLT-II recombinant gene by induction with IPTG using an E, coli hostvector, system was conducted and the correctly processed products with active mature form exhibited 1000-fold higher cytotoxycity for Vero cells than that form original strain.

• The Korean Journal of Mycology
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• v.43 no.4
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• pp.277-280
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• 2015

In August 2015, we collected samples of gray mold from sweet basil growing in Sachunmeon, Gangneung, Gangwon Province, Korea. Symptoms included extensive growth of mycelia with gray conidia on young leaves, stems, and blossoms. The pathogen was isolated from infected leaves and blossoms and the fungus was cultured on potato dextrose agar. For identification of the fungus, morphology and rDNA sequencing analysis of the fungus were performed, which confirmed its pathogenicity according to Koch's postulates. The results of morphological examinations, pathogenicity tests, and the rDNA sequences of the internal transcribed spacer regions (ITS1 and ITS4) and the three nuclear protein-coding genes G3PDH, HSP60, and RPB2 showed that the causal agent was Botrytis cinerea. This is the first report of gray mold caused by Botrytis cinerea on sweet basil in Korea.