• Journal of Life Science
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• v.29 no.5
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• pp.537-544
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• 2019

Genome editing technology employing gene scissors has generated interest in molecular breeding in various fields, and the development of the third-generation gene scissors of the clustered, regularly interspaced short palindromic repeat (CRISPR) system has accelerated the field of molecular breeding through genome editing. In this study, we analyzed the possibility of silkworm molecular breeding using gene scissors by genomic and phenotypic analysis after editing the biogenesis of lysosome-related organelles (BmBLOS) gene of Bakokjam using the CRISPR/Cas9 system. Three types of guide RNAs (gRNA) were synthesized based on the BmBLOS gene sequence of Bakokjam. Complexes of the prepared gRNA and Cas9 protein were formed and introduced into Bombyx mori BM-N cells by electroporation. Analysis of the gene editing efficiency by T7 endonuclease I analysis revealed that the B4N gRNA showed the best efficiency. The silkworm genome was edited by microinjecting the Cas9/B4N gRNA complex into silkworm early embryos and raising the silkworms after hatching. The hatching rate was as low as 18%, but the incidence of mutation was over 40%. In addition, phenotypic changes were observed in about 70% of the G0 generation silkworms. Sequence analysis showed that the BmBLOS gene appeared to be a heterozygote carrying the wild-type and mutation in most individuals, and the genotype of the BmBLOS gene was also different in all individuals. These results suggest that although the possibility of silkworm molecular breeding using the CRISPR/Cas9 system would be very high, continued research on breeding and screening methods will be necessary to improve gene editing efficiency and to obtain homozygotes.

• Journal of Life Science
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• v.30 no.9
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• pp.813-818
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• 2020

The archaeal clusters of orthologous genes (arCOG) algorithm, which identifies common genes among archaebacterial genomes, was used to identify conservative genes among 168 archaebacterial strains. The numbers of conserved orthologs were 14, 10, 9, and 8 arCOGs in 168, 167, 166, and 165 strains, respectively. Among 41 conserved arCOGs, 13 were related to function J (translation, ribosomal structure, and biogenesis), and 10 were related to function L (replication, recombination, and repair). Among the 14 conserved arCOGs in all 168 strains, 6 arCOGs of tRNA synthetase comprised the highest proportion. Of the remaining 8 arCOGs, 2 are involved in reactions with ribosomes, 2 for tRNA synthesis, 2 for DNA replication, and 2 for transcription. These results showed the importance of protein expression in archaea. For the classes or orders having 3 or more members, genomic analysis was performed by averaging the distance values of the conservative arCOGs. Classes Archaeoglobi and Thermoplasmata of the phylum Euryarchaeota showed the lowest and the highest average of distance value, respectively. This study can provides data necessary for basic scientific research and the development of antibacterial agents and tumor control.

• Journal of Life Science
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• v.28 no.2
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• pp.257-264
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• 2018

The YrdC superfamily is a group of proteins that are highly conserved in almost all organisms sequenced so far. YrdC in Escherichia coli was suggested to be involved in ribosome biogenesis, translation termination, cold adaptation, and threonylcarbamoyl adenosine formation in tRNA. In this study, to unambiguously demonstrate that yrdC is essential in E. coli, we constructed two yrdC mutant strains of E. coli and examined their phenotypes. In the temperature-sensitive yrdC mutant strain, cell growth stopped almost immediately under nonpermissive conditions and it appeared to accumulate 16S ribosomal RNA precursors without significant accumulation of 30S ribosomal subunits. We also cloned yeast and human homologs and demonstrated that they complement the E. coli yrdC-deletion strain. By mutational study, we demonstrated that the concave surface in the middle of the YrdC protein plays an important role in E. coli, yeast, and human versions. By comparison of two yrdC-deletion strains, we also unambiguously demonstrated that yrdC is essential for viability in E. coli and that the functions of its yeast and human homologs overlap with that of E. coli YrdC.

• Journal of Life Science
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• v.24 no.10
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• pp.1055-1062
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• 2014

We investigated the expression of cucumber genes involved in lipid mobilization and metabolism during cotyledon development to compare gene activity and to study the direction of carbon (acetyl unit) transport between glyoxysomes and mitochondria. The core metabolic pathway involving 10 genes was examined in four intracellular compartments: glyoxysomes (peroxisomes), mitochondria, chloroplasts, and cytosol. Additionally, we tested the early germination response of dark-grown seedlings and the immediate light response for a further 3 days. According to the reverse transcription polymerase chain reaction (RT-PCR), 3-L-ketoacyl-CoA thiolase 2 (Thio2), isocitrate lyase (ICL), and malate synthase (MS), the genes involved in storage lipid mobilization showed a similar and consistent pattern of gene expression in seedling development. Furthermore, coordinate expression of the A BOUT DE SOUFFLE (BOU) gene with ICL and MS during seedling emergence pointed to a possible secondary route of acetyl unit (acetyl-CoA) transport between peroxisomes and mitochondria in cucumber. The expression of the BOU gene was light dependent, as shown by BOU activity in Arabidopsis, suggesting that the dark condition also results in weak membrane biogenesis. In addition, several genes were active throughout the development of the green cotyledon, even during senescence. In conclusion, this study summarizes oil-seed germination and gene expression during cucumber cotyledon development and proposes an additional route for acetyl unit transport.

• Journal of Microbiology and Biotechnology
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• v.14 no.6
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• pp.1239-1248
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• 2004

The methylotrophic yeast Hansenula polymorpha has been extensively studied as a model organism for methanol metabolism and peroxisome biogenesis. Recently, this yeast has also attracted attention as a promising host organism for recombinant protein production. Here, we describe the fabrication and evaluation of a DNA chip spotted with 382 open reading frames (ORFs) of H. polymorpha. Each ORF was PCR-amplified using gene-specific primer sets, of which the forward primers had 5'-aminolink. The PCR products were printed in duplicate onto the aldehyde-coated slide glasses to link only the coding strands to the surface of the slide via covalent coupling between amine and aldehyde groups. With the partial genome DNA chip, we compared efficiency of direct and indirect cDNA target labeling methods, and found that the indirect method, using fluorescent-labeled dendrimers, generated a higher hybridization signal-to-noise ratio than the direct method, using cDNA targets labeled by incorporation of fluorescence-labeled nucIeotides during reverse transcription. In addition, to assess the quality of this DNA chip, we analyzed the expression profiles of H. polymorpha cells grown on different carbon sources, such as glucose and methanol, and also those of cells treated with the superoxide­generating drug, menadione. The profiles obtained showed a high-level induction of a set of ORFs involved in methanol metabolism and oxidative stress response in the presence of methanol and menadione, respectively. The results demonstrate the sensitivity and reliability of our arrays to analyze global gene expression changes of H. polymorpha under defined environmental conditions.

• Journal of Food Hygiene and Safety
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• v.31 no.2
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• pp.67-73
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• 2016

Resveratrol is a non-flavonoid polyphenol which belongs to the stilbenes group and is naturally generated in several plants in response to damage or fungal invasion. It has been shown in published studies that resveratrol has an anti-adipogenic effect. A good consensus regarding the involvement of a down-regulation of $C/EBP{\alpha}$ and $PPAR{\gamma}$ in this effect has been reached. In addition, different metabolic pathways involved in triacylglycerol metabolism in white adipose tissue have been shown to be regulated by resveratrol. Concerning lipolysis, though this compound in itself seems to be unable to cause lipolysis, it increases lipid mobilization stimulated by ${\beta}-adrenergic$ agents. The increase in brown adipose tissue thermogenesis, and accordingly the associated energy dissipation, can attribute to accounting for the body-fat reducing effect of resveratrol. Besides its effects on adipose tissue, resveratrol can also acts on other organs and tissues. Therefore, it increases mitochondrial biogenesis and accordingly fatty acid oxidation in skeletal muscle and liver. This effect can also attribute to the body-fat reducing effect of this molecule. The present review purposes to collect the evidence concerning the potential mechanisms of action which underlie the anti-obesity effects of resveratrol, acquired either in cultured cells lines and animal models.

• Journal of the Korean Applied Science and Technology
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• v.37 no.4
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• pp.744-754
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• 2020

We investigated the whether endurance exercise and MitoQ intake mediated neuroprotection are associated with mitochondrial function in 1-methyl-4-phenyl-1,2,3,6 tetrahydropyridine(MPTP) -induced mice model of Parkinson's disease. C57BL/6 male mice were randomly assigned to five groups: Normal Conrol(NC, n=10), MPTP Control(MC, n=10), MPTP +MitoQ(MQ, n=10), MPTP + Exercise(ME, n=10) and MPTP + MitoQ + Exercise(MQE, n=10). Exercise intervention groups performed the treadmill exercise for 5days/week for 5 weeks with gradual increase of intensity. MitoQ intake groups consumed the MitoQ at a concentration of 250μmol by dissolving with water during experiment period. Our data demonstrated that ME and MQE group restored MPTP-induced motor dysfunction. In addition, treatment groups(MQ, ME and MQE) increased tyrosine hydroxylase levels, and suppressed the accumulation of α-synuclein levels. Futhermore, treatment groups modulated the mitochondrial function such as upregulated mitochondrial biogenesis, increased antioxidant enzyme, enhanced a anti-apoptotic protein(e.g., BCL2), and reduced a pro-apoptotic protein(e.g., BAX). Taken together, these results suggested that endurance exercise and MitoQ intake-mediated increase in mitochondrial function contributes to improvement of aggravated dopaminergic neuronal, resulting in attenuation of motor function of Parkinson's disease.

• Journal of Life Science
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• v.12 no.5
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• pp.610-621
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• 2002

Conserved genes are importantly used to understand the major function in survival and replication of living organism. This study was focused on identification of conserved genes in microbial species and measuring the degree of conservation. For this purpose, in silico analysis was performed to search conserved genes based on the conservation level within microbial species. The ortholog list of COGs (Clusters of Orthologous Groups of proteins) in NCBI was used and whole genomes of 43 microbial species were included in that list. The distance value, derived from CLUSTALW multiple alignment program, was used as a descriptor of the conservation level of orthologs. It was revealed that 43 microbial genomes hold 72 conserved orthologs in common. The majority(72.2%) of the conserved genes was related to "translation, ribosomal structure and biogenesis" functional category. A GTPase-translation elogation factor(COG0050) was the best conserved gene from the distance value analysis. The 72 conserved genes, found in this research, would be useful not only to study minimal function genes but also new drug target among pathogens and to make a model of the virtual cell.tual cell.

• Journal of Life Science
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• v.26 no.9
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• pp.1097-1104
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• 2016

With the development of next generation sequencing (NGS), large numbers of transcriptional molecules have been discovered. Most transcripts are non -coding RNAs (ncRNAs). Among them, long non-coding RNAs (lncRNAs) with more than 200 nucleotides represent functional RNA molecule that will not be translated into protein. In plants, lncRNAs are transcribed by RNA polymerase II (Pol II) or Pol III, Pol VI and Pol V. After transcription of these lncRNAs, more RNA processing mechanisms such as splicing and polyadenylation occurs. The expression of plant lncRNAs is very low and is tissue specific. However, these lncRNAs are strongly induced by specific external stimuli. Because different external stimuli including environmental stresses induce a large number of plant lncRNAs, these lncRNAs have been gradually considered as new regulatory factors of various biological and development processes such as epigenetic repression, chromatin modification, target mimicry, photomorphogenesis, protein relocalization, environmental stress response, pathogen infection in plants. Moreover, some lncRNAs act as precursor of short RNAs. Although a large number of lncRNAs have been predicted and identified in plants, our current understanding of the biological function of these lncRNAs is still limited and their detailed regulatory mechanisms should be elucidated continuously. Here, we reviewed the biogenesis and regulation mechanisms of lncRNAs and summarized the molecular functions unraveled in plants.

• The Korean Journal of Malacology
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• v.22 no.2
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• pp.109-113
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• 2006

Subcellular localization of a protein containing nuclear localization signals (NLS) has been well studied in many organisms ranging from invertebrates to vertebrates. However, no systematic analysis of NLS-containing proteins available from Mollusks has been reported. Here, we describe in silico screening of NLS-containing proteins using the mollusks database that contains 22,138 amino acids. To screen putative proteins with NLS-motif, we used both predict NLS and perl script. As a result, we have found 266 proteins containing NLS sequences which are about 1.2% out of the entire proteins. On the basis of KOG (The eukaryotic orthologous groups) analysis, we can't predict the precise functions of the NLS-containing proteins. However, we found out that these proteins belong to several types of proteins such as chromatin structure and dynamics, translation, ribosomal structure, biogenesis, and signal transduction mechanism. In addition, we have analysed these sequences based on the classes of mollusks. We could not find many from the species that are the main subjects of phylogenetic studies. In contrast, we noticed that cephalopods has the highest number of NLS-containing proteins. Thus, we have constructed mollusks NLS database and added these information and data to the mollusks database by constructing web interface. Taken together, these information will be very useful for those who are or will be studying NLS-containing proteins from mollusks.