• Journal of Applied Biological Chemistry
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• 제63권2호
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• pp.125-129
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• 2020

Environmental pollution caused by various heavy metals is a serious global problem. To solve this problem, microbial bioremediation of contaminated metals has developed rapidly as an effective strategy when physical and chemical techniques are not suitable. In this study, cadmium (Cd)-tolerant soil bacteria were isolated via artificial induction in laboratory conditions instead of screening bacteria naturally adapted to metal-contaminated soils. Wild-type (WT) bacteria grown in uncontaminated soils were artificially and sequentially adapted to gradually increasing Cd concentrations of up to 15 mM. The resultant cells, named Soil-CdR15, survived at a Cd concentration of 10 mM, whereas WT cells failed to survive with 4 mM Cd on solid media for 2 d. In liquid media containing Cd, the SoilCdR15 cells grew with 15 mM Cd for 7 d, whereas the WT cells could not grow with 5 mM Cd. Both Soil-CdR15 and WT cells removed approximately 35% of Cd at the same capacity from liquid media containing either 0.5 or 1.0 mM Cd over 2 d. In addition to Cd, the Soil-CdR15 cells showed increased resistance to nickel, zinc, and arsenic compared to WT cells. The Soil-CdR cells were identified as Burkholderia sp. by partial sequencing of 16S rRNA. The data presented in this study demonstrate that isolation of heavy metal-tolerant microorganisms via artificial induction in laboratory conditions is possible and may be useful for the application of the microorganisms for the bioremediation of heavy metals.

• 제어로봇시스템학회:학술대회논문집
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• 제어로봇시스템학회 2004년도 ICCAS
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• pp.190-195
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• 2004

We propose a pattern classification algorithm using self-nonself discrimination principle of immune cells and apply it to DNA pattern classification problem. Pattern classification problem in bioinformatics is very important and frequent one. In this paper, we propose a classification algorithm based on the negative selection of the immune system to classify DNA patterns. The negative selection is the process to determine an antigenic receptor that recognize antigens, nonself cells. The immune cells use this antigen receptor to judge whether a self or not. If one composes ${\eta}$ groups of antigenic receptor for ${\eta}$ different patterns, these receptor groups can classify into ${\eta}$ patterns. We propose a pattern classification algorithm based on the negative selection in nucleotide base level and amino acid level. Also to show the validity of our algorithm, experimental results of RNA group classification are presented.

• BMB Reports
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• 제30권3호
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• pp.216-221
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• 1997

Changes in pathogenicity of old and successively-cultured isolates of Fusarium oxysporum f. sp. niveum have been observed and the concept that such cultures will become attenuated is generally accepted. However, the genetic basis for this phenomenon has not been studied. In an effort to identify a DNA marker closely linked to variations, DNA methylation was investigated both before and after the successive transfers of F. o. f. sp. niveum isolates on artificial media. A sector of mycelium in F. o. f. sp. niveum race 2 isolate (TXXID) which showed variation in pigmentation and colonial morphology occurred after 18 successive weekly transfers on potato dextrose agar (PDA). The sector characteristics were stable and did not change after more successive transfers. It was shown that DNA methylation preexists in ribosomal RNA gene (rDNA) of F. o. f. sp. niveum and that additional changes in DNA methylation occurred during successive culturing.

• 한국미생물학회:학술대회논문집
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• 한국미생물학회 2001년도 추계학술대회
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• pp.121-127
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• 2001

Seven cyanobacteria strains (Anabaena macrospora NIERl0016, Oscillatoria sp. NIER10042, Microcystis aeruginosa NIER10015, M. ichtyoblabe BIER10025, BIER10040, M. novacekii NIER10029, M. wesenbergii NIER10068) were tested with four rRNA - targeted oligonucleotide probes labelled with horseradish peroxidase (HRP) and specific for cyanobacteria. Non- fluorescent detection of hybridization signal was used. The hybridization with artificial mixture of cyanobacteria have shown the possibility to use 2 species-specific probes in duplicate hybridization and detection with different colored substrates.

• Journal of Information Processing Systems
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• 제13권2호
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• pp.204-214
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• 2017

Artificial intelligence, especially deep learning technology, is penetrating the majority of research areas, including the field of bioinformatics. However, deep learning has some limitations, such as the complexity of parameter tuning, architecture design, and so forth. In this study, we analyze these issues and challenges in regards to its applications in bioinformatics, particularly genomic analysis and medical image analytics, and give the corresponding approaches and solutions. Although these solutions are mostly rule of thumb, they can effectively handle the issues connected to training learning machines. As such, we explore the tendency of deep learning technology by examining several directions, such as automation, scalability, individuality, mobility, integration, and intelligence warehousing.

• Rapid Communication in Photoscience
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• 제3권4호
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• pp.79-80
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• 2014

We characterized the one-electron reduction of oligodeoxynucleotides with a 2-oxopropyl group on a thymine base ($d^{oxo}T$) and applied the reaction to the radiolytic activation of DNAzyme function. We designed a system in which the DNAzyme function of cleaving mRNA was suppressed by introduction of $d^{oxo}T$ into the strand of DNAzyme. Hypoxic X-irradiation led to recovery of the cleavage ability because the 2-oxopropyl group was removed to form unmodified DNAzyme. We characterized the DNAzyme function by monitoring the fluorescence change of fluorophore- and quencher-labeled target strands. We confirmed that the DNAzyme function could be regulated by hypoxic X-irradiation and the reaction of $d^{oxo}T$.

• 한국연초학회지
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• 제19권2호
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• pp.117-123
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• 1997

Viral coat protein (CP) encoding cDNA with artificial start and stop codons was synthesized by reverse-transcriptase polymerase chain reaction (RT-PCR) from the Korean isolate of potato virus Y-vein nectrosis strain (pVY-VN). To make PVY CP cDNA to untranslatable form, three stop codons were inserted near the start codon by "megaprimer-PCR" method. The untranslatable CP cDNA was subcloned to plant expression vector and transferred to N. tabacum cv. NC82 by Agrobacterium-mediated transformation. Highly resistant plants to PVY infection were screened, based on symptom development after mechanical virus inoculation. By genomic PCR and Southern blot analysis, one or more copies of the untranslatable CP gene were found in all transformants. From northern blot analysis, highly resistant transgenic lines had very low level of CP transcript but susceptible lines had high level, suggesting resistance to PVY infection should be related to RNA-mediated mechanism.mechanism.

• Current Research on Agriculture and Life Sciences
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• 제31권4호
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• pp.245-249
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• 2013

In 2008, leaf blight symptoms were observed on several Chinese chive farms in Sangju. The Pathogenicity of the isolate was confirmed by artificial inoculation, where the pathogen exhibited a strong pathogenicity toward healthy plants. Morphological classification identified the isolate as from the Fusarium genus. For further analysis, PCR and phylogenetic classification were performed with ITS region and 28S rRNA gene which are commonly used for fungal identification. However, the results provided a poor resolution. To solve this problem, we analyzed translation elongation factor 1-alpha (TEF-$1{\alpha}$) gene. The analyzed results using TEF-$1{\alpha}$ gene indicated that the isolate was F. proliferatum. Therefore, it is assumed that TEF-$1{\alpha}$ gene is important when Fusarium sp. was identified using molecular classification method.

• Mycobiology
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• 제41권3호
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• pp.167-169
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• 2013

Black spot of sweet persimmon, caused by Alternaria alternata, occurred in an orchard in Gyeongnam province, Korea in 2012. The symptom was appearance of 0.5 to 4 cm black spots on the surface of fruit. The pathogen was isolated from flesh of disease lesions. The causal agent was identified as A. alternata by morphological characteristics and sequencers of the internal transcribed spacer (ITS) 1 and ITS4 regions of rRNA. Artificial inoculation of the pathogen resulted in development of disease symptoms and the re-isolated pathogen showed characteristics of A. alternata.

• BMB Reports
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• 제31권4호
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• pp.413-417
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• 1998

Transgenic mice containing a bovine ${\beta}-Casein/Human$ lysozyme fusion gene (pBZ) were generated in order to produce human lysozyme in their milk. The expression vector was a quadripartite fusion consisting of a 2 kb upstream DNA of the bovine ${\beta}-casein$ gene, human lysozyme gene, intron II of the rabbit ${\beta}-globin$ gene, and the polyadenylation/termination signals of SV40 DNA. Fertilized mouse zygotes were microinjected with pBZ, then transferred into the oviduct of foster mothers. Out of 20 mice born, 11 survived until postweaning and three were identified as positivetransgenic by Southern blot analysis (one male and two females). The founder mice were mated to BCFl mice to produce transgenic progeny. It was confirmed by RT-PCR and Northern blot analyses that the transgene was specifically expressed in the mammary gland of the founder mice. Furthermore, the artificial introns within the transgenic RNA was proven to be correctly spliced out as judged by RT-PCR analysis. These results indicated that transgenic mice generated in this study properly expressed the human lysozyme RNA in their mammary gland.