• Research in Plant Disease
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• v.26 no.3
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• pp.170-178
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• 2020

Most strawberry viruses exist relatively low titers in tissues, and strawberry tissues include high levels of contamination by polysaccharides and phenolic compounds. These traits make the efficiency of strawberry diagnosis difficult. In this study, we tested different commercially available kits and reagents to secure optimal RNA extraction methods to determine virus detection from strawberry leaves. Total RNA was isolated from leaves of strawberry mottle virus (SMoV)-infected strawberry cultivar 'Mihong'. The efficiency of total RNA for virus diagnosis was confirmed through SMoV detection by one-step or two-step reverse transcription and polymerase chain reaction (RT-PCR). Among those, the RNeasy plant RNA kit was best to isolate RNA and the isolated RNA was good enough for further applications. To ensure a reliable detection for strawberry viruses, synthetic diagnosis clones for major seven strawberry viruses such as strawberry mild yellow edge virus, SMoV, strawberry latent ring spot virus, strawberry crinkle virus, strawberry pallidosis associated virus, strawberry vein banding virus and strawberry necrotic spot virus have been constructed. Based on the synthetic genes in each clone, primer sets for seven strawberry viruses were designed and tested an RT-PCR condition through a simultaneous application of the same annealing temperature that allowed to achieve an efficient and convenient diagnosis.

• Korean Journal of Microbiology
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• v.47 no.2
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• pp.103-109
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• 2011

Pectobacterium carotovorum subsp. carotovorum is the causative agent of soft rot in crops such as potato and cabbages. Loop-mediated isothermal amplification (LAMP) is a simple DNA amplification method, as well as isothermal PCR technique. In this study, a new method for the rapid detection of Pectobacterium carotovorum subsp. carotovorum was developed using LAMP that named PCC-LAMP. Based on lytic murein transglycolase gene of Pectobacterium carotovorum subsp. carotovorum, a set of four primers for LAMP was designed. The optimal PCC-LAMP reaction temperature was established at $61^{\circ}C$. Under standard conditions, PCC-LAMP amplified $1{\times}10^3$ copies of clone PCC-pBX437 per reaction. Further, this method can also assay directly by SYBR Green I without electrophoresis. Amplification was not detected for five other bacterial species. In conclusion, PCC-LAMP may be a useful method for the detection Pectobacterium carotovorum subsp. carotovorum in the field.

• Proceedings of the Korea Society of Environmental Biology Conference
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• 2002.11a
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• pp.119-122
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• 2002

Soil contaminants are common in industrialized sites, They can affect directly soil and indirectly ground water and food. Soil mutagens and carcinogens are of great interest due to their potentially hazardous effects on human health. The aim of this study was to monitor the genotoxicity of contaminated soils, Soil leachates were collected from two polluted sites and one control site in Cheongju. Tradescantia BNL 4430 clone was used as experimental matierials. Chromosomal damages induced by soil leachates were detected by the Tradescantia-micronucleus assay. It is known from the result that Tradescantia-micronucleus assay is an excellent botanical tool for detection of biological risk due to environmental toxicants.

• Journal of Microbiology
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• v.43 no.6
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• pp.572-576
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• 2005

This study focused on detecting catabolic genes for polycyclic aromatic hydrocarbons (PAHs) distributed in the reed rhizosphere of Sunchon Bay, Korea. These marsh and mud environments were severely affected by human activities, including agriculture and fisheries. Our previous study on microbial roles in natural decontamination displayed the possibility that PAH-degrading bacteria, such as Achromobacter sp., Alcaligenes sp., Burkholderia sp. and Pseudomonas sp. play an important decontamination role in a reed rhizosphere. In order to gain further fundamental knowledge on the natural decontamination process, catabolic genes for PAH metabolism were investigated through PCR amplification of dioxygenase genes using soil genomic DNA and sequencing. Comparative analysis of predicted amino acid sequences from 50 randomly selected dioxygenase clones capable of hydroxylating inactivated aromatic nuclei indicated that these were divided into three groups, two of which might be originated from PAH-degrading bacteria. Amino acid sequences of each dioxygenase clone were a part of the genes encoding enzymes for initial catabolism of naphthalene, phenanthrene, or pyrene that might be originated from bacteria in the reed rhizosphere of Sunchon Bay.

• Asian-Australasian Journal of Animal Sciences
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• v.27 no.4
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• pp.561-566
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• 2014

The complete coding sequence of Wild Argali ISG15 cDNA was generated by rapid amplification of cDNA ends. The ISG15 cDNA was 642 bp with an open reading frame of 474 bp, which encoded a 17.47 kDa protein composed of 157 amino acids. Its amino acid sequence shared 97.9%, 80.8%, 91.4%, 94.3%, 78.3% identity with those of ISG15cDNA from Ovis aries (accession no. NM001009735.1), Capra hircus (accession no. HQ329186.1), Bos taurus (accession no. BC102318.1), Bubalus bubalis (accession no. HM543269.1), and Sus scrofa (accession no. EU647216.1), respectively. The entire coding sequence was inserted into the pET-28a vector and expressed in E. coli. The recombinant protein corresponded to the expected molecular mass of 25 kDa as judged by SDS-PAGE, and it was detected in the bacterial inclusion bodies. The expressed protein could be purified by $Ni^{2+}$ chelate affinity chromatography and the results from the lymphocyte proliferation test showed that the product could stimulate lymphocyte proliferation very well (p<0.05), which further confirmed its biological activity.

• Genomics & Informatics
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• v.15 no.4
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• pp.128-135
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• 2017

As next-generation sequencing technologies have advanced, enormous amounts of whole-genome sequence information in various species have been released. However, it is still difficult to assemble the whole genome precisely, due to inherent limitations of short-read sequencing technologies. In particular, the complexities of plants are incomparable to those of microorganisms or animals because of whole-genome duplications, repeat insertions, and Numt insertions, etc. In this study, we describe a new method for detecting misassembly sequence regions of Brassica rapa with genotyping-by-sequencing, followed by MadMapper clustering. The misassembly candidate regions were cross-checked with BAC clone paired-ends library sequences that have been mapped to the reference genome. The results were further verified with gene synteny relations between Brassica rapa and Arabidopsis thaliana. We conclude that this method will help detect misassembly regions and be applicable to incompletely assembled reference genomes from a variety of species.

• Journal of Microbiology and Biotechnology
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• v.20 no.8
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• pp.1179-1184
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• 2010

We report the generation of the first monoclonal antibody that specifically binds to the polysaccharide chitosan. Mice were immunized with a mixture of chitosans, and hybridoma clones were screened for specific binders, resulting in the isolation of a single clone secreting a chitosan-specific IgM, mAbG7. In ELISAs, the antibody could bind to chitosans of varying composition, but demonstrated the highest affinity for chitosans with lower degrees of acetylation (DA) and very poor binding to chitin. We tested the ability of the antibody to bind to chitosan in situ, using preparations of fungal cell walls. Immunofluorescence microscopy confirmed that the antibody bound strongly to the cell walls of fungi with high levels of chitosan, whereas poor staining was observed in those species with cell walls of predominantly chitin or cellulose. The potential use of this antibody for the detection of fungal contamination and the protection of plants against fungal pathogens is discussed.

• Journal of Computing Science and Engineering
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• v.9 no.4
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• pp.190-203
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• 2015

Free and open source software (FOSS) has created a large pool of source codes that can be easily copied to create new applications. However, a copy should preserve copyright notice and license of the original file unless the license explicitly permits such a change. Through software evolution, it is challenging to keep original licenses or choose proper licenses. As a result, there are many potential license violations. Despite the fact that violations can have high impact on protecting copyright, identification of violations is highly complex. It relies on manual inspections by experts. However, such inspection cannot be scaled up with open source software released daily worldwide. To make this process scalable, we propose the following two methods: use machine-based algorithms to narrow down the potential violations; and guide non-experts to manually inspect violations. Using the first method, we found 219 projects (76.6%) with potential violations. Using the second method, we show that the accuracy of crowds is comparable to that of experts. Our techniques might help developers identify potential violations, understand the causes, and resolve these violations.

• Asian Pacific Journal of Cancer Prevention
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• v.13 no.3
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• pp.975-978
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• 2012

P63 is a gene product required in cell cycle regulation which plays vital roles in tumor differentiation. Aims of the present study were to assess the frequency, pattern, sensitivity and specificity of two p63 protein clones P63 4A4 and P63 4A4+Y4A3 in squamous cell carcinomas (SCCs). Thirty cases of head and neck region SCC diagnosed on the basis of H&E staining were examined along with 60 cases of head and neck region biopsies other than squamous cell carcinoma, negative on H&E staining, were taken as control. Immunostaining was performed on slides according to the Thermo Scientific UltraVision LP detection System. P63 4A4+Y4A3 clone is more sensitive 96.6% in comparison to 86% in P63 4A4 with having greater NPV of 98.3%. The results signify the importance of P63 4A4+Y4A3 marker over the old markers and may be used as a confirmatory marker of squamous cell carcinoma.

• The Journal of Korean Society of Virology
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• v.29 no.2
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• pp.99-105
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• 1999

BamHI restriction pattern and genomic library of Herpes simplex virus type 2 (HSV-2) strain G were constructed, and locations of the glycoproteins gB and gD, and tk genes on the fragments were detected by Southern blot analysis. HSV-2 genomic DNAs were cleaved into twenty-seven fragments by BamHI enzyme in the range of 0.72 to 15.08 (total 150.44 kb), which were cloned into the BamHI site of pBluescript SK(+) to construct genome library of the HSV-2. The library was named by the order of the fragment size from smallest one to largest one. HSV-2 glycoprotein gD gene was located in pHLA2-21 and pHLA2-22 recombinant plasmids, gB gene in pHLA2-24 plasmid, and tk gene in pHLA2-11 clone by Southern blot analysis.