• Journal of the Korean Institute of Telematics and Electronics S
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• v.36S no.12
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• pp.10-19
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• 1999

Cellular Automata Neural Systems(CANS) are neural networks based on biological development and evolution. Each neuron of CANS has local connection and acts as a form of pulse according to the dynamics of the chaotic neuron. CANS are generated from initial cells according to the CA rule. In the previous study, to obtain the useful ability of CANS, we make the pattern of initial cells evolve. However, it is impossible to represent all solution space, so we propose an evolving method of CA rule to overcome this defect in this paper. DNA coding has the redundancy and overlapping of gene and is apt for the representation of the rule. In this paper, we show the general expression of CA rule and propose translation method from DNA code to CA rule. The effectiveness of the proposed scheme was verified by applying it to the navigation problem of autonomous mobile robot.

• Fisheries and Aquatic Sciences
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• v.15 no.2
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• pp.107-115
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• 2012

In developing a useful tool to detect parasitic dynamics in an estuarine ecosystem, a denaturing high-performance liquid chromatography (DHPLC) assay was optimized by cloning plasmid DNA from the grass shrimp Palaemonetes pugio, and its two parasites, the trematode Microphallus turgidus and bopyrid isopod Probopyrus pandalicola. The optimal separation condition was an oven temperature of $57.9^{\circ}C$ and 62-68% of buffer B gradient at a flow rate of 0.45 mL/min. A peptide nucleic acid blocking probe was designed to clamp the amplification of the host gene, which increased the amplification efficiency of genes with low copy numbers. Using the DHPLC assay with wild-type genomic, the assay could detect GC Gram positive bacteria and the bopyrid isopod (P. pandalicola). Therefore, the DHPLC assay is an effective tool for surveying parasitic dynamics in an estuarine ecosystem.

• Clinical and Experimental Reproductive Medicine
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• v.36 no.2
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• pp.101-109
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• 2009

Objective: This study was carried out to analyze the amount of telomeric DNA and telomerase activity in early bovine embryos. Methods: The amount of telomeric DNA in early bovine embryos at the 8 cell, morula and blastocyst stages was analyzed by Quantitative Fluorescence In Situ Hybridization (Q-FISH) technique using a bovine telomeric DNA probe. Telomerase activity was analyzed by Telomeric Repeat Amplification Protocol (TRAP assay). Results: The relative amount of telomeric DNA in early bovine embryos was gradually increased from 8 cell to blastocyst stage. It was not significantly associated with the grade of embryo quality. While telomerase activity was detected in the early bovine embryos at these stages, it significantly increased at morula stage and showed maximum activity at the blastocyst stage. Conclusion: The amount of telomeric DNA and the telomerase activity of bovine embryos increase during the progression of early embryogenesis, suggesting a positive correlation between telomeric DNA and telomerase activity. The telomerase activity seems to increase to maintain the levels of telomeric DNA through embryo development which are required for extensive cell division.

• Genomics & Informatics
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• v.15 no.4
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• pp.142-146
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• 2017

More effective production of human insulin is important, because insulin is the main medication that is used to treat multiple types of diabetes and because many people are suffering from diabetes. The current system of insulin production is based on recombinant DNA technology, and the expression vector is composed of a preproinsulin sequence that is a fused form of an artificial leader peptide and the native proinsulin. It has been reported that the sequence of the leader peptide affects the production of insulin. To analyze how the leader peptide affects the maturation of insulin structurally, we adapted several in silico simulations using 13 artificial proinsulin sequences. Three-dimensional structures of models were predicted and compared. Although their sequences had few differences, the predicted structures were somewhat different. The structures were refined by molecular dynamics simulation, and the energy of each model was estimated. Then, protein-protein docking between the models and trypsin was carried out to compare how efficiently the protease could access the cleavage sites of the proinsulin models. The results showed some concordance with experimental results that have been reported; so, we expect our analysis will be used to predict the optimized sequence of artificial proinsulin for more effective production.

• BMB Reports
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• v.38 no.1
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• pp.104-110
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• 2005

We extended the measurable time scale of DNA dynamics to microsecond using $[Ru(phen)_2(dppz)]^{2+}$ (phen = 1,10-phenanthroline, dppz = dipyrido[3,2-a:2',3'-c]phenazine) (RuPD), which displays a mean lifetime near 500 ns. To evaluate the usefulness of this luminophore (RuPD) for probing nucleic acid dynamics, its intensity and anisotropy decays when intercalated into supercoiled and linear pBluescript (pBS) II SK(+) phagemids were examined using frequency-domain fluorometry with a blue light-emitting diode (LED) as the modulated light source. The mean lifetime for the supercoiled phagemids (< $\tau$ > = 489.7 ns) was somewhat shorter than that for the linear phagemids (< $\tau$ > = 506.4 ns), suggesting a more efficient shielding from water by the linear phagemids. The anisotropy decay data also showed somewhat shorter slow rotational correlation times for supercoiled phagemids (997.2 ns) than for the linear phagemids (1175.6 ns). The slow and fast rotational correlation times appear to be consistent with the bending and torsional motions of the phagemids, respectively. These results indicate that RuPD can have applications in studies of both bending and torsional dynamics of nucleic acids.

• Mass Spectrometry Letters
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• v.2 no.3
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• pp.73-75
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• 2011

In the collisionally-activated dissociation of the proton-bound cluster ions of DNA base guanine (G) and cytosine (C), $G{\bullet}{\bullet}H^+{\bullet}{\bullet}C$, the abundance of [$CH^+$] ions was found to be higher than that of [$GH^+$] despite the fact that G has a higher proton affinity than C. This unexpected observation seems to demonstrate another example that the simple kinetic method scheme does not work. We suggest that a kinetic factor or detailed dynamics governing the proton transfer and dissociation should be carefully considered in the applications of the kinetic method to the proton affinity measurements.

• BMB Reports
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• v.57 no.1
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• pp.66-70
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• 2024

Prime editors (PEs), which are CRISPR-Cas9 nickase (H840A)-reverse transcriptase fusion proteins programmed with prime editing guide RNAs (pegRNAs), can not only edit bases but also install transversions, insertions, or deletions without both donor DNA and double-strand breaks at the target DNA. As the demand for in-locus tagging is increasing, to reflect gene expression dynamics influenced by endogenous genomic contexts, we demonstrated that PEs can be used to introduce the hemagglutinin (HA) epitope tag to a target gene locus, enabling molecular and biochemical studies using in-locus tagged plants. To promote genome-wide in-locus tagging, we also implemented a publicly available database that designs pegRNAs for in-locus tagging of all the Arabidopsis genes.

• The Plant Pathology Journal
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• v.28 no.4
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• pp.433-438
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• 2012

Dinoflagellates are considered one of the most abundant and diverse groups of marine microplankton and viruses are recognized as one of the significant factors affecting the plankton dynamics. Here, we report basic characteristics of a new dinoflagellate-infecting virus, Heterocapsa pygmaea DNA virus (HpygDNAV) which infects a toxic dinoflagellate, H. pygmaea. HpygDNAV is a polyhedral large virus (ca. 160-170 nm in diameter) propagating in its host's cytoplasm. Because of the virion size, appearance in thin sections, and propagation characteristics, HpygDNAV is assumed to harbor a large double-stranded DNA genome; i.e., HpygDNAV is most likely a nucleocytoplasmic large DNA virus (NCLDV) belonging to the family Phycodnaviridae. Its infectivity is strain-specific, rather than species-specific, as is the case for other algal viruses. The burst size and latent period are estimated to be roughly 100-250 infectious units $cell^{-1}$ and < 96 h, respectively.

• Proceedings of the Korean Society of Potoscience Conference
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• 2006.06a
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• pp.44-44
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• 2006

• Reproductive and Developmental Biology
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• v.35 no.3
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• pp.281-285
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• 2011

In the present study, we identified differentially methylated region (DMR) upstream of Dnmt1o and Dnmt1s gene in early porcine embryos. Porcine Dnmt1o had at least one DMR which was located between -530 bp to -30 bp upstream from transcription start site of the Dnmt1o gene. DNA methylation analyses of Dnmt1o revealed the DMR to be hypomethylated in oocytes, whereas it was highly methylated in sperm. Moreover, the DMR upstream of Dnmt1o was gradually hypermethylated from oocytes to two cells and dramatically changed in the methylation pattern from four cells to BL stages in an in vivo. In an IVF, the methylation status in the DMR upstream of Dnmt1o was hypermethylated from one cell to eight cells, but demethylated at the Morula and BL stages, indicating that the DNA methylation pattern in the Dnmt1o upstream ultimately changed from stage to stage before the implantation. Next, to elucidate whether DNA methylation status of Dnmt1s upstream is stage-by-stage changed in during porcine early development, we analyzed the dynamics of the DNA methylation status of the Dnmt1s locus in germ cell, or one cell to BL cells. The Dnmt1s upstream was highly methylated in one and eight cells, while less methylated in two, four, morula, and BL cells. Taken together, our data demonstrated that DNA methylation and demethylation events in upstream of Dnmt1o/Dnmt1s during early porcine embryos dramatically occurred, and this change may contribute to the maintenance of genomewide DNA methylation in early embryonic development.