• Journal of fish pathology
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• v.6 no.2
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• pp.93-101
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• 1993

The RNAI mutation of Saccharomyces cerevisia is a recessive and temperature sensitive lethal mutation which interferes with the production of mRNA, rRNA, and tRNA. However, the precise role of RNAI gene have not been revealed until yet. We have cloned rna1-1 mutant gene from rna1-1 mutant yeast strain(R49 ; trpl, ura3-52, rna1-1). The 3.4kb BglII fragment of wild type RNAI clone(81-2-6) contains whole RNAI gene. The genomic southern blotting with BglII digested R49 genomic DNA as a probe shows the unique and identical band with wild type 3.4kb BglII fragment. Therefore, We prepared partial BglII genomic library(3~4kb BglII fragments) into BamH I site of pUC19. The rna 1-1 mutant clone was screened with Digoxigenin(DIG)-lableled probe by high density colony hybridization. The 5'-flanking region of rna1-1 gene was sequenced by dideoxy chain termination method. The 5'-flanking sequence of RNAI gene contains three TATA-like sequence ; TAATA, TATA and TTTTAA at position of -67, -45, and -36 from first ATG codon respectively. The 5'-flanking region of wild type RNA I gene from ATG codon to -103nt was deleted with Bal31 exonuclease digestion, generating $pUC{\Delta}$/RNA I. After constructing $pYEP{\Delta}RNA$ I (consists of -103nt deleting RNA I gene, URA3 gene, $2{\mu}m$ rep. origin), pYEPrna1-1(consists of Xba I fragment of pUCrna1-1. URA3 gene, $2{\mu}m$ rep. origin), and pYEPRNAI. each plasmid was transformed into host strain(trpl, ura3-52, rna1-1) by electroporation, respectively. Yeast transformant carrying $pYEP{\Delta}RNA$ I did not complement the thermal sensitivity of rna1-1 gene. It means that TATA-like sequences in 5'-flanking region is not TATA sequence for transcribing RNAI gene and there may be other essential sequence in upstream region for the transcription of RNAI gene.

• Proceedings of the Korean Society of Developmental Biology Conference
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• 1998.07a
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• pp.32-33
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• 1998

생물체에서 유전외적 변형의 하나인 DNA 메틸화는 cis-acting factor의 조성변화를 통하여 세포특이 유전자의 발현과 virus latency, genomic imprinting, mutagenesis등과 같은 생물학적 효과를 나타내는 것으로 알려져 있다.(reviewed by Olle Heby, 1995). 5-azaCR, 5-azaCdR 그리고 6-azaCR의 처리결과는 배아자체의 DNA 메틸화의 유지가 정상발생에 필수적임을 알 수 있으며, 메틸화에 의한 배아발생 조절기작이 존재함을 암시하고 있다. 이러한 과정에서 5-azaCR과 5-azaCdR은 서로다른 경로를 통하여 배아발생에 관여함을 보여주었다. 즉, 5-azaCdR은 주로 DNA에 incorporation되어 작용하는 것으로 여겨지며, 5-azaCR은 DNA 보다는 RNA에 incorporation되어 작용하는 것으로 나타났다. 그리고, 비록 소수의 유전자만이 조사되었지만, 5-azaCdR의 incorporation에 의한 cis-acting factor의 변화는 전사인자인 c-myc proto-oncogene과 fluid 수송에 관여하는 $Na^{+}$, $K^{+}$-ATPase 유전자의 전사를 억제하지 않았다. 반면, 5-azaCR의 RNA로의 incorporation은 전사인자인 c-myc proto-oncogene의 전사를 억제하였으며, 연이어 fluid 수송에 관련되어있는 $Na^{+}$, $K^{+}$-ATPase 유전자의 전사를 억제하였다. 이것은 아마도 RNA로 incorporation된 5-azaCR은 RNA의 post-transcriptional processing에 영향을 주어 trans-acting factor의 조성을 변화, 전사적 repression을 유발한 것으로 사료된다. 생쥐 착상전 초기배아에서 DNA 메틸화는 short-term하게는 cis-acting factor로써 전사적 수준에서 유전자발현 조절하며, 그리고 유전자발현을 통하여 long-term하게는 배아발생에 관여 할 것이라고 사료된다.

• Korean Journal of Microbiology
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• v.53 no.4
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• pp.286-291
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• 2017

In eukaryotic cells, histone modification is an important mechanism to regulate the chromatin structure. The methylation of the fourth lysine on histone H3 (H3K4) by Set1 complex is one of the various well-known histone modifications. Set1 complex has seven subunits including Swd2, which is known to be important for H2B ubiquitination dependent on H3K4 methylation. Swd2 was reported to regulate Set1's methyltransferase activity by binding to near RNA recognition motif (RRM) domain of Set1 and to act as a component of CPF (Cleavage and Polyadenylation Factors) complex involved in RNA 3' end processing. According to the recent reports, two functions of Swd2 work independently of each other and the lethality of Swd2 knockout strain was known to be caused by its function as a component of CPF complex. In this study, we found that Swd2 could influence the Set1's stability as well as histone methyltransferase activity through the association with RRM domain of Set1. Also, we found that ${\Delta}swd2$ mutant bearing truncated-Set1, which cannot interact with Swd2, lost its lethality and grew normally. These results suggest that the dual functions of Swd2 in H3K4 methylation and RNA 3' end processing are not independent in Saccharomyces cerevisiae.

• Animal Bioscience
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• v.35 no.8
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• pp.1162-1173
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• 2022

Objective: This study aimed to investigate the fermentation profiles, bacterial community and predicted metabolic characteristics of Sudangrass (Sorghum sudanense Stapf.) during ensiling. Methods: First-cutting Sudangrass was harvested at the vegetative stage and ensiled in laboratory-scale silos (1 L capacity). Triplicate silos were sampled after 1, 3, 7, 15, 30, and 60 days of ensiling, respectively. The bacterial communities on day 3 and 60 were assessed through high-throughput sequencing technology, and 16S rRNA-gene predicted functional profiles were analyzed according to the Kyoto encyclopedia of genes and genomes using Tax4Fun. Results: The Sudangrass silages showed good fermentation quality, indicated by higher lactic acid contents, and lower pH, butyric acid and ammonia nitrogen contents. The dominant genus Lactococcus on day 3 was replaced by Lactobacillus on day 60. The metabolism of amino acid, energy, cofactors and vitamins was restricted, and metabolism of nucleotide and carbohydrate was promoted after ensiling. The 1-phosphofructokinase and pyruvate kinase of bacterial community seemed to play important roles in stimulating the lactic acid fermentation, and the promotion of arginine deiminase could help lactic acid bacteria to tolerate the acidic environment. Conclusion: High-throughput sequencing technology combined with 16S rRNA gene-predicted functional analyses revealed the differences during the early and late stages of Sudangrass ensiling not only for distinct bacterial community but also for specific functional metabolites. The results could provide a comprehensive insight into bacterial community and metabolic characteristics to further improve the silage quality.

• The Journal of the Institute of Internet, Broadcasting and Communication
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• v.16 no.3
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• pp.203-211
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• 2016

The genetic code is a key to bio-informatics and to a science of biological self-organizing on the whole. Modern science faces the necessity of understanding and systematically explaining mysterious features of ensembles of molecular structures of the genetic code. This paper is devoted to symmetrical analysis for genetic systems. Mathematical theories of noise-immunity coding and discrete signal processing are based on Jacket matrix methods of representation and analysis of information. Both of the RNA and Jacket Matrix property also have the Element(Block) - wise Inverse Matrices. These matrix methods, which are connected closely with relations of symmetry, are borrowed for a matrix analysis of ensembles of molecular elements of the genetic code. This method is presented for its simplicity and the clarity with which it decomposes a Jacket Matrix in terms of the genetic RNA Codon.

• 대한생식의학회:학술대회논문집
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• 2001.11a
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• pp.116.2-116.2
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• 2001

• Animal cells and systems
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• v.13 no.2
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• pp.235-245
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• 2009

Embryonic stem (ES) cells have a capability to generate all types of cells. However, the mechanism by which ES cells differentiate into specific cell is still unclear. Using microarray technology, the differentiation process in mouse embryonic stem cells was characterized by temporal gene expression changes of mouse ES cells during differentiation in a monolayer culture. A large number of genes were differentially regulated from 1 day to 14 days, and less number of genes were differentially expressed from 14 days to 28 days. The number of up-regulated genes was linearly increased throughout the 28 days of in vitro differentiation, while the number of down-regulated genes reached the plateau from 14 days to 28 days. Most differentially expressed genes were functionally classified into transcriptional regulation, development, extra cellular matrix (ECM),cytoskeleton organization, cytokines, receptors, RNA processing, DNA replication, chromatin assembly, proliferation and apoptosis related genes. While genes encoding ECM proteins were up-regulated, most of the genes related to proliferation, chromatin assembly, DNA replication, RNA processing, and cytoskeleton organization were down-regulated at 14 days. Genes known to be associated with embryo development or transcriptional regulation were differentially expressed mostly after 14 days of differentiation. These results indicate that the altered expression of ECM genes constitute an early event during the spontaneous differentiation, followed by the inhibition of proliferation and lineage specification. Our study might identify useful time-points for applying selective treatments for directed differentiation of mouse ES cells.

• International journal of advanced smart convergence
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• v.8 no.3
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• pp.115-122
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• 2019

Recent and ongoing discoveries of mycoviruses with new properties demand the development of an appropriate research infrastructure to analyze their evolution and classification. In particular, the discovery of negative-sense single-stranded mycoviruses is worth noting in genome types in which double-stranded RNA virus and positive-sense single-stranded RNA virus were predominant. In addition, some genomic properties of mycoviruses are more interesting because they have been reported to have similarities with the pathogenic virus family that infects humans and animals. Genetic information on mycoviruses continues to accumulate in public repositories; however, these databases have some difficulty reflecting the latest taxonomic information and obtaining specialized data for mycoviruses. Therefore, in this study, we developed a bioinformatics-based pipeline to efficiently utilize this genetic information. We also designed a schema for data processing and database construction and an algorithm to keep taxonomic information of mycoviruses up to date. The pipeline and database (termed 'mycoVDB') presented in this study are expected to serve as useful foundations for improving the accuracy and efficiency of future research on mycoviruses.

• The Korean Journal of Pharmacology
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• v.29 no.2
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• pp.225-235
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• 1993

Pituitary LH release has been known to be regulated by the hypothalamic gonadotropin releasing hormone (GnRH) and the gonadal steroid hormones. In addition, neurotransmitters and neuropeptides are actively involved in the control of LH secretion. The alteration in LH release might reflect changes in biosynthesis and/or posttranslational processing of LH. However, little is known about the mechanism by which biosynthesis of LH subunits is regulated, especially at the level of transcription. In order to investigate if ovarian steroid hormones regulate the LH subunit gene expression, ${\alpha}\;and\;LH{\beta}$ steady state mRNA levels were determined in anterior pituitaries of ovariectomized rats. Serum LH concentrations and pituitary LH concentrations were increased markedly with time after ovariectomy. ${\alpha}\;and\;LH{\beta}$ subunit mRNA levels after ovariectomy were increased in a parallel manner with serum LH concentrations and pituitary LH contents, the rise in $LH{\beta}$ subunit mRNA levels being more prominent than the rise in ${\alpha}\;subunit$ mRNA. ${\alpha}\;and\;LH{\beta}$ subunit mRNA levels in ovariectomized rats were negatively regulated by the continuous treatment of ovarian steriod hormones for $1{\sim}4\;days$ and $LH{\beta}\;subunit$ mRNA seemed to be more sensitive to negative feedback of estradiol than progesterone. Treatment of estrogen antagonist, LY117018 or progesterone antagonist, RU486 significantly restroed LH subunit mRNA levels as well as LH release which were suppressed by estradiol or progesterone treatment. These results suggest that ovarian steroids negatively regulate the LH synthesis at the pretranslational level by modulating the steady state levels of ${\alpha}\;and\;LH{\beta}\;subunit$ mRNA and $LH{\beta}\;subunit$ mRNA seemed to be more sensitive to negative feedback action of estradiol than progesterone.

• Korean Journal of Microbiology
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• v.44 no.2
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• pp.93-97
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• 2008

RraA is a recently discovered protein inhibitor that regulates the enzymatic activity of RNase E, which plays a major role in the decay and processing of RNAs in Escherichia coli. It has also been shown to regulate the activity of RNase ES, a functional Streptomyces coelicolor ortholog of RNase E, which has 36% identity to the amino-terminal region of RNase E. There are two open reading frames in S. coelicolor genome that can potentially encode proteins having more than 35.4% similarity to the amino acid sequence of RraA. DNA fragment encoding one of these RraA orthologs, designated as RraAS2 here, was amplified and cloned in to E. coli vector to test whether it has ability to regulate RNase E activity in E. coli cells. Co-expression of RraAS2 partially rescued E. coli cells over-producing RNase E from growth arrest, although not as efficiently as RraA, induced by the increased ribonucleolytic activity in the cells. The copy number of ColEl-type plasmid in these cells was also decreased by 14% compared to that in cells over-producing RNase E only, indicating the ability of RraAS2 to inhibit RNase E action on RNA I. We observed that the expression level of RraAS2 was lower than that of RraA by 4.2 folds under the same culture condition, suggesting that because of inefficient expression of RraAS2 in E. coli cells, co-expression of RraAS2 was not efficiently able to inhibit RNase E activity to the level for proper processing and decay of all RNA species that is required to restore normal cellular growth to the cells over-producing RNase E.