• Research in Plant Disease
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• v.12 no.3
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• pp.213-220
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• 2006

In year 2003, a soybean(Glycine max) sample showing severe dwarfing symptom was collected from a farmers' field in Cheongsong in Korea. The results from the diagnosis of the sample by RT-PCR revealed that it was infected by Soybean dwarf virus(SbDV), SbDV-L81. This study could be the first report of the occurrence of the virus in Korea. To further characterize the virus, the partial nucleotide sequence of the genomic RNA of SbDV-L81 was determined by RT-PCR using species-specific primers. The sequences were analyzed and subsequently compared to previously characterized strains of SbDV based on the pattern of symptom expression and vector specificities. The intergenic region between ORF 2 and 3 and the coding regions of ORF 2, 3 and 4 were relatively similar to those of dwarfing strains(SbDV-DS and DP) rather than those of yellowing strains(SbDV-YS and YP). Likewise, the result from the analysis of 5'-half of the coding region of ORF5 indicated that SbDV-L81 was closely related to strains(SbDV-YP and DP) transmitted by Acyrthosiphon pisum. These data from the natural symptom and the comparisons of five regions of nucleotide sequences of SbDV suggested that SbDV-L81 might be closely related SbDV-DP.

• Journal of Life Science
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• v.20 no.3
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• pp.411-415
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• 2010

Anisakis simplex is one of the parasitic nematodes, and has a complex life cycle in crustaceans, fish, squid or whale. When people eat under-processed or raw fish, it causes anisakidosis and also plays a critical role in inducing serious allergic reactions in humans. However, no web-based database on A. simplex at the level of DNA or protein has been so far reported. In this context, we constructed a web-based database for Anisakis research. To build up the web-based database for Anisakis research, we proceeded with the following measures: First, sequences of order Ascaridida were downloaded and translated into the multifasta format which was stored as database for stand-alone BLAST. Second, all of the nucleotide and EST sequences were clustered and assembled. And EST sequences were translated into amino acid sequences for Nuclear Localization Signal prediction. In addition, we added the vector, E. coli, and repeat sequences into the database to confirm a potential contamination. The web-based database gave us several advantages. Only data that agrees with the nucleotide sequences directly related with the order Ascaridida can be found and retrieved when searching BLAST. It is also very convenient to confirm contamination when making the cDNA or genomic library from Anisakis. Furthermore, BLAST results on the Anisakis sequence information can be quickly accessed. Taken together, the Web-based database on A. simplex will be valuable in developing species specific PCR markers and in studying SNP in A. simplex-related researches in the future.

• Journal of Life Science
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• v.31 no.3
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• pp.356-365
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• 2021

Recently, we sequenced the entire genome of a freshwater agar-degrading bacterium Cellvibrio sp. KY-GH-1 (KCTC13629BP) to explore genetic information encoding agarases that hydrolyze agarose into monomers 3,6-anhydro-L-galactose (L-AHG) and D-galactose. The KY-GH-1 strain appeared to possess nine β-agarase genes and two α-neoagarobiose hydrolase (α-NABH) genes in a 77-kb agarase gene cluster. Based on these genetic information, the KY-GH-1 strain-caused agarose degradation into L-AHG and D-galactose was predicted to be initiated by both endolytic GH16 and GH86 β-agarases to generate NAOS (NA4/NA6/NA8), and further processed by exolytic GH50 β-agarases to generate NA2, and then terminated by GH117 α-NABHs which degrade NA2 into L-AHG and D-galactose. More recently, by employing E. coli expression system with pET-30a vector we obtained three recombinant His-tagged GH50 family β-agarases (GH50A, GH50B, and GH50C) derived from Cellvibrio sp. KY-GH-1 to compare their enzymatic properties. GH50A β-agarase turned out to have the highest exolytic β-agarase activity among the three GH50 isozymes, catalyzing efficient NA2 production from the substrate (agarose, NAOS or AOS). Additionally, we determined that GH117A α-NABH, but not GH117B α-NABH, could potently degrade NA2 into L-AHG and D-galactose. Sequentially, we examined the enzymatic characteristics of GH50A β-agarase and GH117A α-NABH, and assessed their efficiency for NA2 production from agarose and for production of L-AHG and D-galactose from NA2, respectively. In this review, we describe the benefits of recombinant GH50A β-agarase and GH117A α-NABH originated from Cellvibrio sp. KY-GH-1, which may be useful for the enzymatic hydrolysis of agarose for mass production of L-AHG and D-galactose.

• Journal of Life Science
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• v.18 no.8
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• pp.1132-1139
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• 2008

A CpG island is a short stretch of DNA in which the frequency of the CG dinucleotide is higher than other regions. CpG islands are present in the promoters and exonic regions of approximately $30{\sim}60$% of mammalian genes so they are useful markers for genes in organisms containing 5-methylcytosine in their genomes. Recent evidence supports the notion that the hypermethylation of CpG island, by silencing tumor suppressor genes, plays a major causal role in cancer, which has been described in almost every tumor types. In this respect, CpG island search by computational methods is very helpful for cancer research and computational promoter and gene predictions. I therefore developed a window program (called CpGi) on the basis of CpG island criteria defined by D. Takai and P. A. Jones. The program 'CpGi' was implemented in Visual C++ 6.0 and can determine the locations of CpG islands using diverse parameters (%GC, Obs (CpG)/Exp (CpG), window size, step size, gap value, # of CpG, length) specified by user. The analysis result of CpGi provides a graphical map of CpG islands and G+C% plot, where more detailed information on CpG island can be obtained through pop-up window. Two human contigs, i.e. AP00524 (from chromosome 22) and NT_029490.3 (from chromosome 21), were used to compare the performance of CpGi and two other public programs for the accuracy of search results. The two other programs used in the performance comparison are Emboss-CpGPlot and CpG Island Searcher that are web-based public CpG island search programs. The comparison result showed that CpGi is on a level with or outperforms Emboss-CpGPlot and CpG Island Searcher. Having a simple and easy-to-use user interface, CpGi would be a very useful tool for genome analysis and CpG island research. To obtain a copy of CpGi for academic use only, contact corresponding author.

• Tuberculosis and Respiratory Diseases
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• v.45 no.3
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• pp.587-595
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• 1998

Background: Recombinant adenovirus hold promise as vectors to carry therapeutic genes for several reasons: 1) they can infect both dividing and non-dividing cells; 2) they have the ability to directly transduce tissues in vivo; 3) they can easily be produced in high titer; and 4) they have an established record of safety as vaccination material. However, one of the major limitation in the use of adenoviruses is that transgene expression is quite short because adenovirusees insert their DNA genome episomally rather than by chromosomal integration, and an immune response against the virus destroys cells expressing the therapeutic gene. Since sodium butyrate has been reported to induce adenovirus-mediated gene expression, we hypothesized that treatment of tumor cells, transduced with herpes simples virus thymidine kinase(HSVtk) gene using adenoviral vector, with butyrate could augment the effect of gene therapy. Methods: We transduced HSVtk gene, driven by the cytomegalovirus promoter, into REN cell line(human mesothelioma cell line). Before proceeding with the comparison of HSVtk/ganciclovir mediated bystander killing, we evaluated the effect of butyrate on the growth of tumor cells in order to rule out a potential antitumor effect of butyrate alone, and also on expression of HSVtk gene by Western blot analysis. Then we determined the effects of butyrate on bystander-mediated cell killing in vitro. Results: There was no inhibition of growth of cells exposed to butyrate for 24 hours at a concentration of 1.5mM/L. Toxic effects were seen when the concentration of butyrate was greater than 2.0mM/L. Gene expression was more stable and bystander effect was augmented by butyrate treatment of a concentration of 1.5mM/L. Conclusion: These results provide evidence that butyrate can augment the efficiency of cell killing with HSVtk/GCV system by inducing transgene expression and may thus by a promising new approach to improve responses in gene therapy using adenoviral vectors.

• Journal of Plant Biotechnology
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• v.37 no.3
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• pp.313-318
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• 2010

To develop edible vaccines for swine, the embryogenic calli (type II) derived from HiII genotype were inoculated with A. tumefaciens strain C58C1 containing the binary vector pMYV611, 613, 616, and V621, 622 and 623 respectively. Six of those vectors carry nptII gene which confers resistance to paromomycin and apxIIA gene producing ApxII toxin which is generated in various serum types of A. pleuropneumoniae as a target gene. The 4,120 callus clones for pMYV611, 5,959 callus clones for pMYV613, 7,581 callus clones for pMYV616, 52,329 callus clones for V621, 48,948 callus clones for V622, and 56,188 callus clones for V623 were inoculated. The frequency of positive response clone was confirmed into range of 2.3% - 4.4% for each vectors by NPTII ELISA kit assay, and the selected callus clones of them were finally 3 callus clones from pMYV611 (0.07%), 4 callus clones from pMYV613 (0.07%), 2 callus clones from pMYV616 (0.03%), 51 callus clones from V621 (0.1%), 72 callus clones from V622 (0.15%), and 102 callus clones from V623 (0.18%) respectively. From the selected callus clones of each binary vector, the integration of the apxIIA gene into maize genome was detected from 2 plants of pMYV613 and 2 plants of V623 by Southern blot analysis.

• Journal of Plant Biotechnology
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• v.43 no.3
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• pp.347-358
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• 2016

Brassinosteroid (BR), a plant steroid hormone, plays key roles in numerous growth and developmental processes as well as tolerance to both abiotic and biotic stress. To understand the biological networks involved in BR-mediated signaling pathways and stress tolerance, we performed comparative genome-wide transcriptome analysis of a constitutively activated BR bes1-D mutant with an Agilent Arabidopsis $4{\times}44K$ oligo chip. As a result, we newly identified 1,091 (562 up-regulated and 529 down-regulated) significant differentially expressed genes (DEGs). The combination of GO enrichment and protein network analysis revealed that stress-related processes, such as metabolism, development, abiotic/biotic stress, immunity, and defense, were critically linked to BR signaling pathways. Among the identified gene sets, we confirmed more than a 6-fold up-regulation of NB-ARC and FLS2 in bes1-D plants. However, some genes, including TIR1, TSA1 and OCP3, were down-regulated. Consistently, BR-activated plants showed higher tolerance to drought stress and pathogen infection compared to wild-type controls. In this study, we newly developed a useful, comprehensive method for large-scale identification of critical network and gene sets with global transcriptome analysis using a microarray. This study also showed that gain of function in the bes1-D gene can regulate the adaptive response of plants to various stressful conditions.

• Journal of Animal Science and Technology
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• v.46 no.4
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• pp.537-546
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• 2004

Adiponectin is adipocyte complement-related protein which is highly specialized to play important roles in metabolic and honnonal processes. This protein, called GBP-28, AdipoQ, and Acrp30, is encoded by the adipose most abundant gene transcript 1 (APM1) which locates on human chromosome 3q27 and mouse chromosome 16. In order to determine chromosomal localization of the porcine APM1, we carried out PCR analysis using somatic cell hybrid panel as well as porcine whole genome radiation hybrid (RH) panel. The result showed that the porcine APM1 located on chromosome 13q41 or 13q46-49. These locations were further investigated with the two point analysis of RH panel, revealed the most significant linked marker (LOD score 20.29) being SIAT1 (8 cRs away), where the fat-related QTL located. From the SSCP analysis of APM1 using 8 pig breeds, two distinct SSCP types were detected from K~ native and Korean wild pigs. The determined sequences in Korean native and Korean wild pigs showed that two nucleotide positions (T672C and C705G) were substituted. The primary sequence of the porcine APM1 has 79 to 87% identity with those of human, mouse, and bovine APM1. The domain structures of the porcine APM1 such as signal sequence, hypervariable region, collagenous region. and globular domain are also similar to those of mammalian genes.

• Journal of Life Science
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• v.22 no.12
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• pp.1644-1650
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• 2012

The aim of this study was to screen the polymorphisms and distribution of each genotype of insertion/ deletion (indel) markers which were found in a preliminary comparative study of bovine genomic sequence databases. Comparative bioinformatic analyses were first performed between the nucleotide sequences of Bovine Genome Project and those of expressed sequence tag (EST) database, and a total of fifty-one species of indel markers were screened. Of these, forty-two indel markers were evaluated, and nine informative indel markers were ultimately selected for population analysis. Nucleotide sequences of each marker were re-sequenced and their polymorphic patterns were typed in six cattle breeds: Holstein, Angus, Charolais, Hereford, and two Korean native cattle breeds (Hanwoo and Jeju Black cattle). Cattle breeds tested in this study showed polymorphic patterns in eight indel markers but not in the Indel-15 marker in Charolais and Holstein. The results of analysis for Jeju Black cattle (JBC) population indicated an observed heterozygosity (Ho) that was highest in HW_G1 (0.600) and the lowest in Indel_29 (0.274). The PIC value was the highest in HW_G4 (0.373) and lowest in Indel_6 (0.305). These polymorphic indel markers will be useful in supplying genetic information for parentage tests and traceability and to develop a molecular breeding system for improvement of animal production in cattle breeds as well as in the JBC population.

• Korean Journal of Breeding Science
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• v.41 no.2
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• pp.106-114
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• 2009

In maize, knowledge of genetic diversity and genetic relationships among elite inbred lines is an significant impact on the selection of parental lines for hybrid varieties. Genetic diversity and genetic relationships among 11 parental inbred lines of Korean waxy and normal corn varieties were analyzed using 50 SSR markers distributed over the whole genome. A total of 171 allele bands were detected with an average of 3.4 alleles per locus. Number of allele bands per locus ranged from two to six and gene diversity varied from 0.165 to 0.900 with an average of 0.596 depending on the SSR loci. The cluster tree recognized three major groups with 61.6% genetic similarity. Group I includes 7 inbred lines (KL103, HW1, HW4, HW6, HW7, HW8, HW9), with similarity coefficients of between 0.616 and 0.730. Group II includes 2 inbred lines (HF1, HF2), with similarity coefficients of 0.959. Group III includes 2 inbred lines (HW3, HW5), with similarity coefficients of 0.713. The present study indicates that the SSR markers chosen for this analysis are effective for the assessment of genetic diversity and genetic relationships among 11 parental inbred lines.