• The Plant Pathology Journal
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• v.18 no.5
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• pp.251-258
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• 2002

A potyvirus was isolated from cultivated Iris plants showing leaf streak mosaic symptom. Reverse transcription and polymerase chain reaction (RT-PCR) product of 1 kb long which encoded partial nuclear inclusion B and N-terminal region of viral coat protein (CP) genes for potyviruses was successfully amplified with a set of potyvirus-specific degenerate primers with viral RNA samples from the infected leaves: The RT-PCR product was cloned into the plasmid vector and its nucleotide sequences were determined. The nucleotide sequence of a CDNA clone revealed that the virus was an isolate of Ornithogalum moseic virus (OrMV) based on BLAST search analysis and was denoted as OrMV Korean isolate (OrMV-Ky). To further characterize the CP gene of the virus, a pair of OrMV-specific primers was designed and used for amplification of the entire CP gene of OrMV-Kr, The virus was easily and reliably detected from virus-infected Iris leaves by using the RT-PCR with the set of virus-specific primers. The RT-PCR product of the CP gene of the virus was cloned and its sequences were determined from selected recombinant CDNA clones. Sequence analysis revealed that the CP of OrMV-Kr consisted of 762 nucleotides, which encoded 253 amino acid residues. The CP of OrMV-Ky has 94.1-98.0% amino acid sequence identities (20 amino acid alterations) with that of other three isolates of OrMV, Two NT rich potential N-glycosylation motif sequences, NCTS and NWTM, and a DAC triple box responsible for aphid transmission were conserved in CPs of all the strains of OrMV. The virus has 58.5-86.2% amino acid sequence identities with that of other 16 potyviruses, indicating OrMV to be a distinct species of the genus. OrMV-Ky was the most related with Pterostylia virus Yin the phylogenetic tree analysis of CP at the amino acid level. This is the first report on the occurrence of OrMV in Iris plants in Korea. Data in this study indicate that OrMV is found in cultivated Iris plants, and may have mixed infection of OrMV and Iris severe mosaic virus in Korea.

• Korean Journal of Medicinal Crop Science
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• v.22 no.5
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• pp.339-348
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• 2014

The transcriptomes of four ginseng accessions such as Cheonryang (Korean ginseng cultivar), Yunpoong (Korean ginseng cultivar), G03080 (breeding line of Korean ginseng), and P. quinquefolius (American ginseng) was characterized. As a result of sequencing, total lengths of the reads in each sample were 156.42 Mb (Cheonryang cultivar), 161.95 Mb (Yunpoong cultivar), 165.07 Mb (G03080 breeding line), and 166.48 Mb (P. quinquefolius). Using a BLAST search against the Phytozome databases with an arbitrary expectation value of 1E-10, over 20,000 unigenes were functionally annotated and classified using DAVID software, and were found in response to external stress in the G03080 breeding line, as well as in the Cheonryang cultivar, which was associated with the ion binding term. Finally, unigenes related to transmembrane transporter activity were observed in Cheonryang and P. quinquefolius, which involves controlling osmotic pressure and turgor pressure within the cell. The expression patterns were analyzed to identify dehydrin family genes that were abundantly detected in the Cheonryang cultivar and the G03080 breeding line. In addition, the Yunpoong cultivar and P. quinquefolius accession had higher expression of heat shock proteins expressed in Ricinus communis. These results will be a valuable resource for understanding the structure and function of the ginseng transcriptomes.

• Korean Journal of Environmental Agriculture
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• v.36 no.4
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• pp.241-248
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• 2017

BACKGROUND: RNA interference (RNAi) eliminates or decreases gene expression by disrupting the target mRNA or by interfering with translation. Recently, RNAi technique was applied to generate new crop traits which provide protection against pests. To establish the environmental risk assessment protocol of RNAi LMO in lab scale, we developed dsRNA expression system using E. coli and tested acute oral toxicity assay to honey. METHOD AND RESULTS: The dsRNA expression vector, L4440, was chosen and cloned 240 bp of Snf7 and GFP gene fragment. To develop the maximum dsRNA induction condition in E. coli, we tested induction time, temperature and IPTG concentration in media. To estimate the risk assessment of dsRNA to honey bee, it has been selected and cultured with dsRNA supplement for 48 hours according to OECD guideline. As a result, the optimum condition of dsRNA induction was $37^{\circ}C$, 4 hours and 0.4 mM IPTG concentration and the difference between Snf7 and GFP dsRNA molecules from E. coli was not significant in survival and behavior to honey bee. Furthermore, blast search results indicated that effective match of predicted dsRNA fragments were not existed in honey bee genome. CONCLUSION: In this study, we developed and tested the acute oral toxicity of dsRNA using E. coli expression system to honey bee.

• Korean Journal of Food Science and Technology
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• v.34 no.2
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• pp.283-289
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• 2002

This study was performed to search for potential microorganism that has rapid fermenting and physiological function from anchovy sauce. We isolated three bacterial strains, JM-1, JM-2, and JM-3 with proteolytic and fibrinolytic activity from anchovy sauce. Among the 3 bacterial strains, JM-3 showed the strongest proteolytic and fibrinolytic activity. Bacterial strain JM-3 was gram-positive rod, motile and formed endospore. The 16S rRNA of bacterial strain JM-3 was amplified by PCR and then its sequence was determined by ABI 310 genetic analyzer. The 16S rRNA sequence of bacterial strain JM-3 was compared to BLAST DNA database and identified to Bacillus subtilis with 99% of homology. The optimum temperature, pH and NaCl concentration for growth of B. subtilis JM-3 were $40^{\circ}C$, 5.0 and 0%, respectively. The optimum temperature, pH and NaCl concentration for proteolytic and fibrinolytic enzyme production of B. subtilis JM-3 were same as optimum conditions for growth. At 20% of NaCl concentration which is common NaCl concentration of fish sauce, B. subtilis JM-3 showed about 60% of proteolytic and fibrinolytic activity of 0% NaCl concentration. From above results, we found that B. subtilis JM-3 will be able to used for starter of functional fish sauce.

• KSBB Journal
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• v.17 no.4
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• pp.370-375
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• 2002

Isolation of a gene and determination of its expression pattern are essential in understanding its function. Among the genes localized in 12ql3, stSG3435 EST was chosen to study its expression pattern. The full-length CDNA was cloned by screening of human brain CDNA library and its sequence was determined by serial deletion followed by automated sequencing of the clones with overlapping fragments. The sequence analysis revealed that stSG 3435 CDNA displayed 100% identity to human MYGI and 86% identity to mouse melanocyte proliferation gene-1 (Gamm 1) originally identified from melanocyte, suggesting that MYGI determined by Northern blot analysis revealed the strongest expression in testes with ubiquitous expression in all the tissues tested. In order to investigate the cellular localization of its protein product, the green fluorescence protein gene was fused into the full-length coding sequence of MYGI, Transfection of the fusion construct followed by confocal microscopy resulted in the green fluorescence signal as a punctate state in cytoplasm indication that MYGI was localized in one of the cellular organelles.

• Journal of the korean academy of Pediatric Dentistry
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• v.33 no.2
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• pp.304-310
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• 2006

Prevotella intermedia is one of the most frequently implicated pathogens in human periodontal disease and has a requirement for hemin for growth. This study has identified a hemin-binding P. intermedia protein by expression of a P. intermedia genomic library in Escherichia coli, a bacterium which does not require or transport exogenous hemin. The genomic library of P. intermedia was constructed into plasmid pUC18, transformed into Escherichia coli strain $DH5{\alpha}$, and screened for recombinant clones using heminbinding activity by plating onto hemin-containing agar. Approximately 5,000 recombinant E. coli colonies were screened onto LB-amp-hemin agar, single clone(pHem1) was exhibited a clearly pigmented phonotype. The 2.5kb insert DNA of pHem1 was determined by restriction enzyme mapping. Southern blot analysis of BamHI, BglII, EcoRI, HindIII and PstI-digested P. intermedia DNA indicated that single copy of the gene was present in the genome. Northern blot analysis revealed that the size of transcript was approximately 1.8 kb. The cloned gene contained a single ORF, consisting of approximately 850-residue amino acids. A BLAST search of the Institute for Genomic Research genes with similar nucleotide sequence revealed no significant similarity It needs further investigation to clarify the mechanisms of heme uptake in P. intermedia.

• Microbiology and Biotechnology Letters
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• v.40 no.1
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• pp.66-69
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• 2012

Five strains out of 200 candidate strains (SG 1-9, 1-12, SG 2-8, 2-10, and 2-17) were selected to determine their antifungal activity against Raffaelea quercus-mongolicae. The 16S rDNA sequences of the five strains were determined by sequencing analysis and analyzed by the homology of the blast program at NCBI. The homology search showed that SG 1-9 and 1-12 had a 98% homology with Streptomyces cinnamoneus and 98% homology with Burkholderia cepacia, while SG 2-8, 2-10, and 2-17 had a 99% homology with Streptomyces fradiae, a 97% homology with Staphylococcus epidermidis, and a 99% homology with Staphylococcus epidermidis. Out of the five selected strains, organic extract and protein extracts of SG2-17 strain broth were employed to determine antifungal activity against Raffaelea quercus-mongolicae. The organic extract exhibited antifungal activity, but the protein extracts did not demonstrate such an activity. Three organic solvents, butanol, benzene, and ethyl acetate, were also used for determination of antifungal activities. The activity measurements revealed that benzene extract possessed the greatest inhibitory effect on the growth of Raffaelea quercus-mongolicae, with the next highest being butanol extract, and ethyl acetate extract being the lowest.

• Journal of Food Hygiene and Safety
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• v.36 no.4
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• pp.331-341
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• 2021

DNA barcode sequences of commercial seafood products, which are difficult to morphologically discriminate, were analyzed to determine cases of food fraud. The gene sequences were analyzed by amplifying the COX I (cytochrome C oxidase subunit I) gene region of mitochondrial DNA, which is mainly used for species identification. The DNA barcode sequences were compared with the gene sequence of each fish registered in the US National Center for Biotechnology. A total of 46 processed seafood products (12 Pagrus majo, 4 Oplegnathus fasciatus, 7 Dentex tumifrons, 2 Acanthopagrus schlegelii, 7 Oreochromis niloticus, 6 Branchiostegus japonicus, 8 Branchiostegus albus) were investigated. Having DNA sequence identity of more than 97% was judged as the same species. As a result of this study, no cases of forgery and alteration were detected. However, some disparities in the commercial names used in local markets and the standard names given in the Korea Food Code were found, which may cause confusion for consumers. It is therefore suggested that the standard name or scientific name be displayed on seafood product labels.

• Fisheries and Aquatic Sciences
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• v.26 no.9
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• pp.558-568
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• 2023

Vibrio vulnificus is an aquatic bacterium causing septicemia and wound infection in humans. To understand this pathogen at the genomic level, it was performed whole genome sequencing of a cefoxitin-resistant strain, V. vulnificus 1908-10 possessing virulence-related genes (vvhA, viuB, and vcgC) isolated from Gadeok island coastal seawater in South Korea. The genome of V. vulnificus 1908-10 consisted of two circular contigs and no plasmid. The total genome size was estimated to be 5,018,425 bp with a guanine-cytosine (GC) content of 46.9%. We found 119 tRNA and 34 rRNA genes respectively in the genome, along with 4,352 predicted protein sequences. Virulence factor (VF) analysis further revealed that V. vulnificus 1908-10 possess various virulence genes in classes of adherence, antiphagocytosis, chemotaxis and motility, iron uptake, quorum sensing, secretion system, and toxin. In the comparison of the presence/absence of virulence genes, V. vulnificus 1908-10 had fur, hlyU, luxS, ompU, pilA, pilF, rtxA, rtxC, and vvhA. Of the 30 V. vulnificus comparative strains, 80% of the C-genotype strains have all of these genes, whereas 40% of the E-genotype strains have all of them. In particular, pilA were identified in 80% of the C-type strains and 40% of the E-type strains, showing more difference than other genes. Therefore, V. vulnificus 1908-10 had similar VF characteristics to those of type C strains. Multifunctional-autoprocessing repeats-in-toxin (MARTX) toxin of V. vulnificus 1908-10 contained 8 A-type repeats (GXXGXXXXXG), 25 B.1-type repeats (TXVGXGXX), 18 B2-type repeats (GGXGXDXXX), and 7 C-type repeats (GGXGXDXXX). The National Center for Biotechnology Information (NCBI) Basic Local Alignment Search Tool (BLAST) showed that the RtxA protein of V. vulnificus 1908-10 had the effector domain in the order of cross-liking domain (ACD)-C58_PaToxP-like domain- α/β hydrolase-C58_PaToxP-like domain.

• The Sea:JOURNAL OF THE KOREAN SOCIETY OF OCEANOGRAPHY
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• v.15 no.1
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• pp.25-35
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• 2010

The biodiversity of eukaryotic plankton has commonly been used to evaluate the status of aquatic ecosystems. Therefore, an accurate and rapid method for species identification is needed to reveal the biodiversity of environmental water samples. To date, molecular methods have provided a great deal of information that has enabled identification of the hidden biodiversity in environmental samples. In this study, we utilized environmental polymerase chain reaction (PCR) and constructed the 18S nuclear ribosomal RNA clone library from environmental water samples in order to develop more efficient methods for species identification. For the molecular analysis, water samples were collected from the Seonakdong River (Gimhae Bridge) and the coast of Namhae，(Namhaedo). Colony PCR and restriction fragment length polymorphism of PCR (PCR-RFLP) were then adopted to isolate unique clones from the 18S rDNA clone library. Restriction fragment length polymorphism pattern analysis of the Gimhae Bridge sample revealed 44 unique clones from a total of 60 randomly selected clones, while analysis of the Namhae sample revealed 27 unique clones from 150 clones selected at random. A BLAST search and subsequent phylogenetic analysis conducted using the sequences of these clones revealed hidden biodiversity containing a wide range of taxonomic groups (Heterokontophyta (7), Ciliophora (23), Dinophyta (1), Chytridiomycota (1), Rotifera (1) and Arthropoda (11) in the Gimhae Bridge samples Ciliophora (4), Dinophyta (3), Cryptophyta (1), Arthropoda (19) in the Namhae samples). Therefore, the molecular monitoring method developed here can provide additional information regarding the biodiversity and community structure of eukaryotic plankton in environmental samples and helps construct a useful database of biodiversity for aquatic ecosystems.