• Clinical and Experimental Reproductive Medicine
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• v.48 no.4
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• pp.303-310
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• 2021

Decorin (DCN) is a proteoglycan belonging to the small leucine-rich proteoglycan family. It is composed of a protein core containing leucine repeats with a glycosaminoglycan chain consisting of either chondroitin sulfate or dermatan sulfate. DCN is a structural component of connective tissues that can bind to type I collagen. It plays a role in the assembly of the extracellular matrix (ECM), and it is related to fibrillogenesis. It can interact with fibronectin, thrombospondin, complement component C1, transforming growth factor (TGF), and epidermal growth factor receptor. Normal DCN expression regulates a wide range of cellular processes, including proliferation, migration, apoptosis, and autophagy, through interactions with various molecules. However, its aberrant expression is associated with oocyte maturation, oocyte quality, and poor extravillous trophoblast invasion of the uterus, which underlies the occurrence of preeclampsia and intrauterine growth restriction. Spatiotemporal hormonal control of successful pregnancy should regulate the concentration and activity of specific proteins such as proteoglycan participating in the ECM remodeling of trophoblastic and uterine cells in fetal membranes and uterus. At the human feto-maternal interface, TGF-β and DCN play crucial roles in the regulation of trophoblast invasion of the uterus. This review summarizes the role of the proteoglycan DCN as an important and multifunctional molecule in the physiological regulation of oocyte maturation and trophoblast migration. This review also shows that recombinant DCN proteins might be useful for substantiating diverse functions in both animal and in vitro models of oogenesis and implantation.

• Journal of Microbiology and Biotechnology
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• v.34 no.6
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• pp.1322-1327
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• 2024

The accurate and rapid detection of methicillin-resistant Staphylococcus aureus (MRSA) holds significant clinical importance. This work presents a new method for detecting methicillin-resistant Staphylococcus aureus (S. aureus) in clinical samples. The method uses an aptamer-based colorimetric assay that combines a recognizing probe to identify the target and split DNAzyme to amplify the signal, resulting in a highly sensitive and direct analysis of methicillin-resistance. The identification of the PBP2a protein on the membrane of S. aureus in clinical samples leads to the allosterism of the recognizing probe, and thus provides a template for the proximity ligation of split DNAzyme. The proximity ligation of split DNAzyme forms an intact DNAzyme to identify the loop section in the L probe and generates a nicking site to release the loop sequence ("3" and "4" fragments). The "3" and "4" fragments forms an intact sequence to induce the catalytic hairpin assembly, exposing the G-rich section. The released the G-rich sequence of LR probe induces the formation of G-quadruplex-hemin DNAzyme as a colorimetric signal readout. The absorption intensity demonstrated a strong linear association with the logarithm of the S. aureus concentration across a wide range of 5 orders of magnitude dynamic range under the optimized experimental parameters. The limit of detection was calculated to be 23 CFU/ml and the method showed high selectivity for MRSA.

• Proceedings of the KSAR Conference
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• 2003.06a
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• pp.27-27
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• 2003

A diversified and concentrative approach of methylation player can be one of the most powerful studies in the understanding of global epigenetic modifications. Previous studies have suggested that DNA methylation contributes to transcriptional silencing through the several DNA methylation-mediated repression systems by hypermethylation, including methyltransferases (DNMTs), DNA methyltransferase association protein 1 (DMAPl), methyl-CpG binding domain (MBD), and histone deacetylases (HDACs). Assembly of these regulatory protein complexes act sequentially, reciprocally, and interdependently on the newly composed DNA strand through S phase. Therefore, these protein complexes have a role in coupling DNA replication to the designed turn-off system in genome. In this study, we attempted to address the role of DNA methylation by the functional analysis of the methyltransferase molecule, we described the involvement of DMAP1 and DNMTs in cell divistion and the effect of their loss. We also described distinct patterns that DMAP1 and DNMTs are spatially reorganized and displaced from condensing chromosomes as cells progress through mitosis in HeLa cell, COS7, and HIH3T3 cell cycle progressions. DNMT1, DNMT3b, and DMAP1 do not stably contact the genetic material during chromosome compaction and repressive expression. These finding show that the loss of activities of DNMTs and DMAP1 occure stage specifically during the cell cycle, may contribute to the integral balance of global DNA methylation. This is consistent with previous studies resulted in decreased histone acetyltransferases and HDACs, and differs from studies resulted in increased histone methyltransferases. Our results suggest that DNA methylation by DNMTs and DMAP1 during mitosis acts to antagonize hypermethylation by which this mark is epigenetical mitotic-specific methylation.

• Asian-Australasian Journal of Animal Sciences
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• v.31 no.2
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• pp.189-197
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• 2018

Objective: Hemicastration is a unilateral orchiectomy to remove an injured testis, which can induce hormonal changes and compensatory hypertrophy of the remaining testis, and may influence spermatogenesis. However, the underlying molecular mechanisms are poorly understood. Here, we investigated the impact of hemicastration on remaining testicular function. Methods: Prepubertal mice (age 24 days) were hemicastrated, and their growth was monitored until they reached physical maturity (age 72 days). Subsequently, we determined testis DNA methylation patterns using reduced representation bisulfite sequencing of normal and hemicastrated mice. Moreover, we profiled the testicular gene expression patterns by RNA sequencing (RNA-seq) to examine whether methylation changes affected gene expression in hemicastrated mice. Results: Hemicastration did not significantly affect growth or testosterone (p>0.05) compared with control. The genome-wide DNA methylation pattern of remaining testis suggested that substantial genes harbored differentially methylated regions (1,139) in gene bodies, which were enriched in process of protein binding and cell adhesion. Moreover, RNA-seq results indicated that 46 differentially expressed genes (DEGs) involved in meiotic cell cycle, synaptonemal complex assembly and spermatogenesis were upregulated in the hemicastration group, while 197 DEGs were downregulated, which were related to arachidonic acid metabolism. Integrative analysis revealed that proteasome 26S subunit ATPase 3 interacting protein gene, which encodes a protein crucial for homologous recombination in spermatocytes, exhibited promoter hypomethylation and higher expression level in hemicastrated mice. Conclusion: Global profiling of DNA methylation and gene expression demonstrated that hemicastration-induced compensatory response maintained normal growth and testicular morphological structure in mice.

• Journal of Sericultural and Entomological Science
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• v.51 no.2
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• pp.191-196
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• 2013

This study was aimed for development of a useful genes that has a transcript expressional specificity in the early embryonic stage of the silkworm, Bombyx mori. We constructed and analyzed a full-length cDNA library from silkworm's eggs which after a lapse of 2 ~ 6 hours post oviposit. A total 960 clones were randomly selected, and the 5' ends of the inserts were sequenced to generate 652 expressed sequence tags(EST). 334 unique ESTs were generated after the assembly of 652 ESTs. The annotation of 334 unique ESTs by BLAST search revealed that 156(47%) of the sequences represented known genes, whereas 178(53%) of the sequences has no matches in the database. Of the 156 known genes, the most abundant genes were heat shock protein hsp20.8 gene(12 times) and ubiqutin-like protein gene(11 times). The functional groups of these ESTs with matches in the database were constructed according to their putative molecular functions. Among thirteen functional categories, the largest groups were protein synthesis(9.6%) and cellular organization( 8.1%). Further defined studies on molecular functions and biological roles of their promoters will give us wellfined information and its application.

• Proceedings of the Korean Vacuum Society Conference
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• 2013.08a
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• pp.91-91
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• 2013

Imagine a world where we could biomanufacture hybrid nanomaterials having atomic-scale resolution over functionality and architecture. Toward this vision, a fundamental challenge in materials science is how to design and synthesize protein-like material that can be fully self-assembled and exhibit information-specific process. In an ongoing effort to extend the fundamental understanding of protein structure to non-natural systems, we have designed a class of short peptides to fold like proteins and assemble into defined nanostructures. In this talk, I will talk about new strategies to drive the self-assembled structures designing sequence of peptide. I will also discuss about the specific interaction between proteins and inorganics that can be used for the development of new hybrid solar energy devices. Splitting water into hydrogen and oxygen is one of the promising pathways for solar to energy convertsion and storage system. The oxygen evolution reaction (OER) has been regarded as a major bottleneck in the overall water splitting process due to the slow transfer rate of four electrons and the high activation energy barrier for O-O bond formation. In nature, there is a water oxidation complex (WOC) in photosystem II (PSII) comprised of the earthabundant elements Mn and Ca. The WOC in photosystem II, in the form of a cubical CaMn4O5 cluster, efficiently catalyzes water oxidation under neutral conditions with extremely low overpotential (~160 mV) and a high TOF number. The cluster is stabilized by a surrounding redox-active peptide ligand, and undergo successive changes in oxidation state by PCET (proton-coupled electron transfer) reaction with the peptide ligand. It is fundamental challenge to achieve a level of structural complexity and functionality that rivals that seen in the cubane Mn4CaO5 cluster and surrounding peptide in nature. In this presentation, I will present a new strategy to mimic the natural photosystem. The approach is based on the atomically defined assembly based on the short redox-active peptide sequences. Additionally, I will show a newly identified manganese based compound that is very close to manganese clusters in photosystem II.

• Animal Bioscience
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• v.34 no.6
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• pp.975-984
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• 2021

Objective: Inbreeding depression of reproduction is a major concern in the conservation of native chicken genetic resources. Here, based on the successful development of strongly inbred (Sinb) and weakly inbred (Winb) Langshan chickens, we aimed to evaluate inbreeding effects on reproductive traits and identify candidate genes involved in inbreeding depression of reproduction in Langshan chickens. Methods: A two-sample t-test was performed to estimate the differences in phenotypic values of reproductive traits between Sinb and Winb chicken groups. Three healthy chickens with reproductive trait values around the group mean values were selected from each of the groups. Differences in ovarian and hypothalamus transcriptomes between the two groups of chickens were analyzed by RNA sequencing (RNA-Seq). Results: The Sinb chicken group showed an obvious inbreeding depression in reproduction, especially for traits of age at the first egg and egg number at 300 days (p<0.01). Furthermore, 68 and 618 differentially expressed genes (DEGs) were obtained in the hypothalamus and ovary between the two chicken groups, respectively. In the hypothalamus, DEGs were mainly enriched in the pathways related to vitamin metabolism, signal transduction and development of the reproductive system, such as the riboflavin metabolism, Wnt signaling pathway, extracellular matrix-receptor interaction and focal adhesion pathways, including stimulated by retinoic acid 6, serpin family F member 1, secreted frizzled related protein 2, Wnt family member 6, and frizzled class receptor 4 genes. In the ovary, DEGs were significantly enriched in pathways associated with basic metabolism, including amino acid metabolism, oxidative phosphorylation, and glycosaminoglycan degradation. A series of key DEGs involved in folate biosynthesis (gamma-glutamyl hydrolase, guanosine triphosphate cyclohydrolase 1), oocyte meiosis and ovarian function (cytoplasmic polyadenylation element binding protein 1, structural maintenance of chromosomes 1B, and speedy/RINGO cell cycle regulator family member A), spermatogenesis and male fertility (prostaglandin D2 synthase 21 kDa), Mov10 RISC complex RNA helicase like 1, and deuterosome assembly protein 1) were identified, and these may play important roles in inbreeding depression in reproduction. Conclusion: The results improve our understanding of the regulatory mechanisms underlying inbreeding depression in chicken reproduction and provide a theoretical basis for the conservation of species resources.

• Journal of Life Science
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• v.31 no.6
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• pp.568-573
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• 2021

This study identified genomic factors associated with endoplasmic reticulum protein (ERp)29 gene expression in a genome-wide association study (GWAS) of genetic variants, including single-nucleotide polymorphisms (SNPs). In total, 373 European genes from the 1000 Genomes Project were analyzed. SNPs with an allelic frequency of less than or more than 5% were removed, resulting in 5,913,563 SNPs including in the analysis. The following expression quantitative trait loci (eQTL) from the long noncoding RNA LOC105372577 were strongly associated with ERp29 expression: rs6138266 (p<4.172e10), rs62193420 (p<1.173e10), and rs6138267 (p<2.041e10). These were strongly expressed in the testis and in the brain. The three eQTL were identified through a transcriptome-wide association study (TWAS) and showed a significant association with ERp29 and osteosarcoma amplified 9 (OS9) expression. Upstream sequences of rs6138266 were recognized by ChIP-seq data, while HaploReg was used to demonstrate how its regulatory DNA binds upstream of transcription factor 1 (USF1). There were no changes in the expression of OS9 or USF1 following ER stress.

• Journal of Life Science
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• v.30 no.1
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• pp.88-95
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• 2020

Using a random arbitrarily primed polymerase chain reaction, messenger RNA expression levels were assessed after exposure to 10% (v/v) toluene for 8 hr in solvent-tolerant Pseudomonas sp. BCNU 106. Among the 100 up-expressed products, 50 complementary DNA fragments were confirmed to express repeatedly; these were cloned and then sequenced. Blast analysis revealed that toluene stimulated an adaptive increase in the gene expression level in association with transcriptions such as LysR family of transcriptional regulators and RNA polymerase factor sigma-32. The expression of catalase and Mn2+/Fe2+ transporter genes functionally associated with inorganic ion transport and metabolism increased, and the increased expression of type IV pilus assembly PilZ and multi-sensor signal transduction histidine kinase genes, functionally categorized into signal transduction and mechanisms, was also demonstrated under toluene stress. The gene expression level of beta-hexosaminidase in association with carbohydrate transport and metabolism increased, and those of DNA polymerase III subunit epsilon, DNA-3-methyladenine glycosylase II, DEAD/DEAH box helicase domain-containing protein, and ABC transporter also increased after exposure to toluene in DNA replication, recombination, and repair, and even in defense mechanism. In particular, the RNAs corresponding to the ABC transporter, Mn2+/Fe2+ transporter, and the β-hexosaminidase gene were confirmed to be markedly induced in the presence of 10% toluene. Thus, defense mechanism, cellular ion homeostasis, and biofilm formation were shown as essential for toluene tolerance in Pseudomonas sp. BCNU 106.

• Journal of the Korea Institute of Information and Communication Engineering
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• v.10 no.12
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• pp.2329-2334
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• 2006

In this paper, we proposed a method complementing failure of combining DNA fragments, defect of conventional contig assembly programs. In the proposed method, very long DNA sequence data are made into a prototype of fragment of about 700 bases that can be analyzed by automatic sequence analyzer at one time, and then matching ratio is calculated by comparing a standard prototype with 3 fragmented clones of about 700 bases generated by the PCR method. In this process, the time for calculation of matching ratio is reduced by Compute Agreement algorithm. Two candidates of combined fragments of every prototype are extracted by the degree of overlapping of calculated fragment pairs, and then degree of combination is decided using a fuzzy reasoning method that utilizes the matching ratios of each extracted fragment, and A, C, G, T membership degrees of each DNA sequence, and previous frequencies of each A, C, G, T. In this paper. DNA sequence combination is completed by the iteration of the process to combine decided optimal test fragments until no fragment remains. For the experiments, fragments or about 700 bases were generated from each sequence of 10,000 bases and 100,000 bases extracted from 'PCC6803', complete protein genome. From the experiments by applying random notations on these fragments, we could see that the proposed method was faster than FAP program, and combination failure, defect of conventional contig assembly programs, did not occur.