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

• Genomics & Informatics
• /
• v.12 no.3
• /
• pp.105-113
• /
• 2014

A subset of mammalian genes differ functionally between two alleles due to genomic imprinting, and seven such genes (Peg3, Usp29, APeg3, Zfp264, Zim1, Zim2, Zim3) are localized within the 500-kb genomic interval of the human and mouse genomes, constituting the Peg3 imprinted domain. This Peg3 domain shares several features with the other imprinted domains, including an evolutionarily conserved domain structure, along with transcriptional co-regulation through shared cis regulatory elements, as well as functional roles in controlling fetal growth rates and maternal-caring behaviors. The Peg3 domain also displays some unique features, including YY1-mediated regulation of transcription and imprinting; conversion and adaptation of several protein-coding members as ncRNA genes during evolution; and its close connection to human cancers through the potential tumor suppressor functions of Peg3 and Usp29. In this review, we summarize and discuss these features of the Peg3 domain.

• Proceedings of the Ginseng society Conference
• /
• 2002.10a
• /
• pp.96-112
• /
• 2002

In the present study, we have investigated the effects of centrally administered ginsenoside Rc or Rgl on the modulation of NMDA receptor and $GABA_A$ receptor binding in rat brain. The NMDA receptor binding was analyzed by quantitative autoradiography using $[^3H]MK-801$ binding, and $GABA_A$ receptor bindings were analyzed by using $[^3H]muscimol\;and\;[^3H]flunitrazepam$ in rat brain slices. Rats were infused with ginsenoside Rc or Rg1 ($10\;{\mu}g/10{\mu}l/hr$, i.c.v.) for 7 days, through pre-implanted cannula by osmotic minipumps (Alzet, model 2ML), The levels of $[^3H]MK-801$ binding were highly decreased in part of cortex and cingulated by ginsenoside Rc and Rgl. The levels of $[^3H]muscimol$ binding were strongly elevated in almost all regions of frontal cortex by the treatment of ginseoside Rc but decreased by ginsenoside Rg 1. However, the $[^3H]flunitrazepam$ binding was not modulated by ginsenoside Rc or ginsenoside Rgl infusion. These results suggest that prolonged infusion of ginsenoside could differentially modulate $[^3H]MK-801\;and\;[^3H]muscimol$ binding in a region-specific manner. Also, we investigated the influence of centrally administered ginsenoside on the regulation of mRNA levels of the family of NMDA receptor subtypes (NR1, NR2A, NR2B, NR2C) by in situ hybridization histochemistry in the rat brain. The level of NR1 mRNA is significantly increased in temporal cortex, caudate putamen, hippocampus, and granule layer of cerebellum in Rgl-infused rats as compared to control group. The level of NR2A mRNA is elevated in the frontal cortex. In contrast, it was decreased in CAI area of hippocampus in Rgl-infused rats. However, there was no significant change of NR1 and NR2A mRNA levels in Rc-infused rats. The level of NR2B mRNA is elevated in cortex, caudate putamen, and thalamus in both Rc- and Rg-infused rats. In contrast, NR2B level is decreased in CA3 in Rgl-infused rats. The level of NR2C mRNA is increased in the granule layer of cerebellum in only Rg1 but not Rc infused rats. These results show that structure difference of ginsenoside may diversely affect the modulation of expression of NMDA receptor subunit mRNA after infusion into cerebroventricle in rats.

• The Journal of the Institute of Internet, Broadcasting and Communication
• /
• v.16 no.5
• /
• pp.229-233
• /
• 2016

In this paper, we present the four genetic nitrogenous bases of C, U(T), A, G to matrices and describe the structures from $4{\times}4$ RNA(ribose nucleic acid) to $8{\times}8$ DNA((deoxyribose nucleic acid) matrices. we analysis a deoxyribose nucleic acid (DNA) double helix based on the block circulant Hadamard-Jacket matrix (BCHJM). The orthogonal BCHJM is anti-symmetric pair complementary of the core DNA. The block circulant ribonucleic acid (RNA) repair damage reliability is better than the conventional double helix. In case of k=4 and N=1, the reliability of block circulant complementarity is 93.75%, and in case of k=4 and N=4, it is 98.44%. Therefore it improves 4.69% than conventional case of double helix.

• Clinical and Experimental Vaccine Research
• /
• v.12 no.2
• /
• pp.156-171
• /
• 2023

Purpose: The development of vaccines that confer protection against multiple avian influenza A (AIA) virus strains is necessary to prevent the emergence of highly infectious strains that may result in more severe outbreaks. Thus, this study applied reverse vaccinology approach in strategically constructing messenger RNA (mRNA) vaccine construct against avian influenza A (mVAIA) to induce cross-protection while targeting diverse AIA virulence factors. Materials and Methods: Immunoinformatics tools and databases were utilized to identify conserved experimentally validated AIA epitopes. CD8⁺ epitopes were docked with dominant chicken major histocompatibility complexes (MHCs) to evaluate complex formation. Conserved epitopes were adjoined in the optimized mVAIA sequence for efficient expression in Gallus gallus. Signal sequence for targeted secretory expression was included. Physicochemical properties, antigenicity, toxicity, and potential cross-reactivity were assessed. The tertiary structure of its protein sequence was modeled and validated in silico to investigate the accessibility of adjoined B-cell epitope. Potential immune responses were also simulated in C-ImmSim. Results: Eighteen experimentally validated epitopes were found conserved (Shannon index <2.0) in the study. These include one B-cell (SLLTEVETPIRNEWGCR) and 17 CD8⁺ epitopes, adjoined in a single mRNA construct. The CD8⁺ epitopes docked favorably with MHC peptidebinding groove, which were further supported by the acceptable ∆G_bind (-28.45 to -40.59 kJ/mol) and Kd (<1.00) values. The incorporated Sec/SPI (secretory/signal peptidase I) cleavage site was also recognized with a high probability (0.964814). Adjoined B-cell epitope was found within the disordered and accessible regions of the vaccine. Immune simulation results projected cytokine production, lymphocyte activation, and memory cell generation after the 1st dose of mVAIA. Conclusion: Results suggest that mVAIA possesses stability, safety, and immunogenicity. In vitro and in vivo confirmation in subsequent studies are anticipated.

• Korean Journal of Microbiology
• /
• v.47 no.3
• /
• pp.209-217
• /
• 2011

Archaeal communities were investigated using 454 pyrosequencing technology based on 16S rRNA gene in 11 samples collected from six different full-scale anaerobic digesters. Observed operational taxonomic units (OTUs) estimated from the archaeal 16S rRNA gene sequences were 13-55 OTUs (3% cutoff) which was corresponded to 29-89% of Chao1 richness estimates. In the anaerobic digesters there were archaeal sequences within the orders Thermoproteales, Thermoplasmatales, Desulfurococcales as well as within the orders Methanomicrobiales, Methanobacteriales, Methanococcales, Methanosarcinales, and Methanocellales, which are known to produce methane. Among these orders, Methanococcales known to produce methane using hydrogen was the predominant taxon and constituted 51.8-99.7% of total sequences. All samples showed a very similar community structure (Pearson correlation coefficient=0.99) except for one sample based on a heat map analysis. In addition, canonical correspondence analysis correlating archaeal communities to the environmental variables demonstrated that digester temperature and total solids removal rate were the two important explanatory variables. Overall results suggested that environmental and operational variables of anaerobic digester are important factors determining archaeal diversity and community structure.

• Parasites, Hosts and Diseases
• /
• v.58 no.1
• /
• pp.73-79
• /
• 2020

Echinostoma revolutum is a zoonotic food-borne intestinal trematode that can cause intestinal bleeding, enteritis, and diarrhea in human and birds. To identify a suspected E. revolutum trematode from a red-crowned crane (Grus japonensis) and to reveal the genetic characteristics of its mitochondrial (mt) genome, the internal transcribed spacer (ITS) and complete mt genome sequence of this trematode were amplified. The results identified the trematode as E. revolutum. Its entire mt genome sequence was 15,714 bp in length, including 12 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes and one non-coding region (NCR), with 61.73% A+T base content and a significant AT preference. The length of the 22 tRNA genes ranged from 59 bp to 70 bp, and their secondary structure showed the typical cloverleaf and D-loop structure. The length of the large subunit of rRNA (rrnL) and the small subunit of rRNA (rrnS) gene was 1,011 bp and 742 bp, respectively. Phylogenetic trees showed that E. revolutum and E. miyagawai clustered together, belonging to Echinostomatidae with Hypoderaeum conoideum. This study may enrich the mitochondrial gene database of Echinostoma trematodes and provide valuable data for studying the molecular identification and phylogeny of some digenean trematodes.

• Childhood Kidney Diseases
• /
• v.3 no.2
• /
• pp.109-116
• /
• 1999

Purpose: Insulin-like growth factor(IGF)-I and -II are peptide growth factor whose activity is modulated by interaction with the family of six IGF-binding proteins(IGFBPs). IGF-I is detected in rat kidney and has metabolic and growth effects. This study was designed to examine temporal expression of IGFBPs in kidney during renal development and postischemic regeneration in rat. Method: The expression of IGFBPs in kidney during renal development from 15th day of gestation to adult life by using Northern blot analysis. We also examined the renal IGF-IGFBP axis in uremic rat by using Northern blot and immunohistochemistry. Results: The mRNA of IGFBP-1 and -3 were not or barely detected in fetal stages. However, the mRNA level of IGFBP-1 and -3 were increased gradually from day 7 after birth to adult. In contrast, the mRNA of IGFBP-2 and -5 were highly expressed in fetal stages and maintained almost same levels until day 7 (IGFBP-2) or day 30 (IGFBP-5) after birth, then their levels decreased markedly. The mRNA of IGFBP-4 were expressed moderately in fetal kidney and increased gradually after birth. Interestingly, the mRNA of IGFBP-1 and-4 were induced up to 3-5 fold during maximum regeneration period and were recovered to normal levels after acute ischemic injury. In contrast, the mRNA level of IGFBP-3 and-IGFBPrP-1 were decreased slightly at 1 day after ischemic injury, then recovered to normal level during maximum regeneration period. Conclusion: There were differential expressions of IGFBPs in kidney that can modulate IGF action on developing, differentiating, maintaining, and regenerating renal structure and function.

• Journal of the Korean Magnetic Resonance Society
• /
• v.22 no.3
• /
• pp.71-75
• /
• 2018

The CRISPR-Cas system is the adaptive immune system in bacteria and archaea against invading phages or foreign plasmids. In the type II CRISPR-Cas system, an endonuclease Cas9 cleaves DNA targets of phages as directed by guide RNA comprising crRNA and tracrRNA. To avoid targeting and destruction by Cas9, phages employ anti-CRISPR (Acr) proteins that act against host bacterial immunity by inactivating the CRISPR-Cas system. Here we report the backbone $^1H$, $^{15}N$, and $^{13}C$ resonance assignments of AcrIIA4 that inhibits endonuclease activity of type II-A Listeria monocytogenes Cas9 and also Streptococcus pyogenesis Cas9 using triple resonance nuclear magnetic resonance spectroscopy. The secondary structures of AcrIIA4 predicted by the backbone chemical shifts show an ${\alpha}{\beta}{\beta}{\beta}{\alpha}{\alpha}$ fold, which is used to determine the solution structure.

• Journal of Microbiology
• /
• v.44 no.4
• /
• pp.432-438
• /
• 2006

Twelve actinomycete strains were isolated from Egyptian soil. The isolated actinomycete strains were then screened with regard to their potential to generate antibiotics. The most potent of the producer strains was selected and identified. The cultural and physiological characteristics of the strain identified. the strain as a member of the genus Streptomyces. The nucleotide sequence of the 16S rRNA gene (1.5kb) of the most potent strain evidenced a 99% similarity with Streptomyces spp. and S. aureofaciens 16S rRNA genes, and the isolated strain was ultimately identified as Streptomyces sp. MAR01. The extraction of the fermentation broth of this strain resulted in the isolation of one major compound, which was active in vitro against gram-positive, gram-negative representatives and Candida albicans. The chemical structure of this bioactive compound was elucidated based on the spectroscopic data obtained from the application of MS, IR, UV, $^1H$ NMR, $^{13}C$ NMR, and elemental analysis techniques. Via comparison to the reference data in the relevant literature and in the database search, this antibiotic, which had a molecular formula of $C_{19}H_{29}NO_2$ and a molecular weight of 303.44, was determined to differ from those produced by this genus as well as the available known antibiotics. Therefore, this antibiotic was designated Meroparamycin.