• Journal of Life Science
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• v.29 no.1
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• pp.123-128
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• 2019

The use of 16S rDNA is commonplace in the determination of prokaryotic species. However, it has limitations, and there are few studies at the genus level. We investigated conserved genes and metabolic pathways at the genus level in 28 strains of 13 genera of prokaryotes using the COG database (conserved genes) and MetaCyc database (metabolic pathways). Conserved genes compared to total genes (core genome) at the genus level ranged from 27.62%(Nostoc genus) to 71.76%(Spiribacter genus), with an average of 46.72%. The lower ratio of core genome meant the higher ratio of peculiar genes of a prokaryote, namely specific biological activities or the habitat may be varied. The ratio of common metabolic pathways at the genus level was higher than the ratio of core genomes, from 58.79% (Clostridium genus) to 96.31%(Mycoplasma genus), with an average of 75.86%. When compared among other genera, members of the same genus were positioned in the closest nodes to each other. Interestingly, Bacillus and Clostridium genera were positioned in closer nodes than those of the other genera. Archaebacterial genera were grouped together in the ortholog and metabolic pathway nodes in a phylogenetic tree. The genera Granulicella, Nostoc, and Bradyrhizobium of the Acidobacteria, Cyanobacteria, and Proteobacteria phyla, respectively, were grouped in an ortholog content tree. The results of this study can be used for (i) the identification of common genes and metabolic pathways at each phylogenetic level and (ii) the improvement of strains through horizontal gene transfer or site-directed mutagenesis.

• Korean Journal of Ecology and Environment
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• v.54 no.3
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• pp.247-256
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• 2021

Understanding the selective feeding behavior of zooplankton on phytoplankton is essential for evaluating the nutrient cycle and energy flow in the food web. Although many studies have been conducted regarding the feeding behaviors of zooplankton through gut content analyses, there are limitations in the visual identification of digested contents using a microscope. DNA techniques have been applied to overcome these limitations since they can detect and amplify small amounts of prey DNA remaining in the gut contents. We designed a method to extract prey DNA from the gut contents of the whole body of the copepod specimen and tested the resolution of DNA identification for the prey phytoplankton. The common brackish species, Sinocalanus tenellus, were collected from Saemangeum Reservoir in different sites and seasons, and gut content DNA was extracted using 2.5% bleach treatment for 2 min for removal of potential contamination sources existing in preserved specimens without dissolution of the body. The sequences of the extracted gut contents were confirmed using BLASTn suite based on the NCBI database. The phytoplankton species detected in the gut showed temporal and spatial differences. Although DNA analysis of small copepod gut contents has been suggested as an effective method to examine the dynamics of primary prey sources at the genus or species level, uncertainties such as misidentification and limitations in the detailed information of the composition still exist.

• Korean Journal of Plant Resources
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• v.16 no.1
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• pp.82-88
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• 2003

Genomic RNA sequence of a tobamovirus infecting Eutrema wasabi plant(TMV-W) was determined. The RNA is composed 6,298 nucleotide and contains four OREs encoding the protein of 180KD(OREI), 130KD(ORE2),30KD(ORF3) and 18KD(coat protein, ORF4). ORE4, ORF 3, ORF 2 and ORF 1 are overlaped by 130, 20 and 40 nucleotides, and the overapping region can be folded into a stable hairpin styucture. This includes the 3'non-coding region of 238 nucleotides, coat protein gene(537 nucleotides,179 amino acid), 30KD movement protein gene(825 nucleotides, 275 amino acid), 13(IKD protein gene(1,896 nucleotides, 632 amino acid) and 180KD protein gene(2,958 nucleotides, 986 amino acid). The genomic RNA sequence was compared with homologous regions of eleven other tobamoviruses. TMV-WTE was similar to TMV-WSF(98.6%) in nucleotide sequence.

• Journal of the Korean Institute of Intelligent Systems
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• v.11 no.5
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• pp.426-432
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• 2001

This paper is implementation of cellular automata neural network system using evolving hardware concept. This system is a living creatures'brain based on artificial life techniques. Cellular automata neural network system is based on the development and the evolution, in other words, it is modeled on the ontogeny and phylogney of natural living things. The phylogenetic mechanism are fundamentally non-deterministic, with the mutation and recombination rate providing a major source of diversity. Ontogeny is deterministic and local physics. Cellular automata is developed from initial cells, and evaluated in given environment. And genetic algorithms take a part in adaptation process. In this paper we implement this system using evolving hardware concept. Evolving hardware is reconfigurable hardware whose configuration si under the control of an evolutionary algorithm. We design genetic algorithm process for evolutionary algorithm and cells in cellular automata neural network for the construction of reconfigurable system. The effectiveness of the proposed system if verified by applying it to Exclusive-OR.

• Journal of Life Science
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• v.20 no.10
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• pp.1563-1568
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• 2010

In the course of a research concerning the molecular mechanism of hypocotyl elongation that occurs during soybean seedling growth in darkness, we have generated a number of ESTs from a cDNA library prepared from the hypocotyls of dark-grown soybean seedlings. Comparison of the ESTs assigned a cDNA clone as a putative plastidic ATP-binding-cassette (ABC) protein homologue. The soybean GmNAP1 protein contains an N-terminal transit peptide which targets it into the chloroplast. The transcription level of the GmNAP1 gene was investigated under continuous red light, continuous far-red light, and complete darkness. The main function of this NAP1 protein is the transport of protoporphyrin IX which is the precursor of chlorophyll from the cytoplasm to the chloroplast. The GmNAP1 gene was transferred into the Arabidopsis under the CaMV 35S promoter. The chlorophyll level of this transgenic Arabidopsis plant was much higher than the chlorophyll level of the wild type Arabidopsis plant.

• Journal of Life Science
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• v.9 no.1
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• pp.50-57
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• 1999

STATs activated by various cytokine and growth factors trigger a quick response in the nucleus and induce changes in gene expression. We have found the sequences homologous to STAT binding site in the 5'-flanking region of the D-raf gene. In this study, we examined role of the STAT binding site in D-raf gene promoter activity in vivo by using transgenic flies. The reporter plasmid pDraf-STATmut-lacZ was constructed by fusing D-raf promoter fragment having the base-substituted STAT binding site with the lacZ gene in a P-element vector. Transgenic flies bearing the Draf-STATmut-lacZ fusion genes were established by P-element mediated transformation. The expression of lacZ in transgenic flies bearing Draf-STATmut-lacZ fusion genes carrying base substitution in STAT site throughout various developmental stages was extensively reduced in comparison with that in transgenic flies bearing wild type Draf-lacZ fusion gene. These results show that the STAT binding site plays an important role in regulation of the D-raf gene.

• Journal of Life Science
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• v.23 no.4
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• pp.595-601
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• 2013

The clusters of orthologous groups of proteins (COG) algorithm was applied to identify essential proteins in eukaryotes and to measure the degree of conservation. Sixty-three orthologous groups, which were conserved in 66 microbial genomes, enlarged to 104 eukaryotic orthologous groups (KOGs) and 71 KOGs were conserved at the nuclear genome of 7 eucaryotes. Fifty-four of 71 translation-related genes were conserved, highlighting the importance of proteins in modern organisms. Translation initiation factors (KOG0343, KOG3271) and prolyl-tRNA synthetase (KOG4163) showed high conservation based on the distance value analysis. The genes of Caenorhabditis elegans appear to harbor high genetic variation because the genome showed the highest variation at 71 conserved proteins among 7 genomes. The 71 conserved genes will be valuable in basic and applied research, for example, targeting for antibiotic development.

• Journal of Life Science
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• v.17 no.6 s.86
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• pp.772-777
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• 2007

A rice OsLeuD gene for small subunit of 3-isopropylmalate isomerase (IPMI) (EC 4.2.1.33) has been isolated. OsLeuD gene is located on 109.3 cM of chromosome 2. OsLeuD gene was expressed abundantly in metabolically active organs including leaves and developing seeds, indicating that OsLeuD gene expression is developmentally regulated. The cDNA of OsLeuD gene was coded for 257 amino acids which showed 58% and 48% homology to small subunits of IPMI in OsLeuD genes of cyanobacteria and green sulfur bacteria, respectively. The molecular character of OsLeuD is closely related to those of photosynthetic bacteria rather than those of eukaryotes including fungi and yeast. This suggests that OsLeuD gene in chromosomal genome of plants may possibly be originated from chloroplast genome.

• Journal of Life Science
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• v.19 no.7
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• pp.866-870
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• 2009

Fascin, a cytoskeleton actin binding protein, functions in cell adhesion and cell migration. Fascin is also known as a candidate biomarker for various cancers, however, regulatory mechanisms of fascin expression remains little understood. In this study, we found an abnormal bristle phenotype, which is similar to that of the Drosophila fascin mutant, in Drafmutant flies. Hence, we investigated whether fascin expression is regulated by Raf signaling. RT-PCR and Western blot analysis showed that Drosophila fascin expression was down-regulated in Draf mutant flies and the level was increased in larvae expressing the oncogenic form of Draf (Draf$^{got}$) under the GAL4-UAS system. Immunostaining analysis showed increased fascin in the hemocytes over-expressing Draf$^{got}$. Our results indicate that fascin expression is regulated by Raf signaling and suggest that Raf signaling may play an important role in the actin cytoskeleton-associated developmental process and tumor progression via regulation of fascin gene.

• Journal of Wellness
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• v.7 no.4
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• pp.177-186
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• 2012

The purpose of this study was to find out how Accumulation of Short Duration exercises influence on expression of apoptosis genes in a mouse skeletal muscle. The subjects, ICR-type mice, were divided into three cohorts, Accumulation of Short Duration exercise group, continuous aerobic exercise group, and control group. Accumulation of Short Duration exercise group performed wheel-running for fifteen minutes respectively in the morning and afternoon three times a week. Continuous exercise group performed wheel-running for thirty minutes three times a week. Both split and continuous groups completed the wheel-running trials for sixteen weeks. To identify the difference of apoptosis expression between groups, the data colleted from the skeletal muscle were analysed by one way ANOVA. Analyses of the data revealed that significant differences of apoptosis concentration in both continuous and Accumulation of Short Duration exercise groups, there was a notable differences were observed in control group.