• Molecules and Cells
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• v.21 no.1
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• pp.63-75
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• 2006

The 5′-region of Potato virus X (PVX) RNA, which contains an AC-rich, single-stranded region and stem-loop structure 1 (SL1), affects RNA replication and assembly. Using Systemic Evolution of Ligands by EXponential enrichment (SELEX) and the electrophoretic mobility shift assay, we demonstrate that SL1 interacts specifically with tobacco protoplast protein extracts (S100). The 36 nucleotides that correspond to the top region of SL1, which comprises stem C, loop C, stem D, and the tetra loop (TL), were randomized and bound to the S100. Remarkably, the wild-type (wt) sequence was selected in the second round, and the number of wt sequences increased as selection proceeded. All of the selected clones from the fifth round contained the wt sequence. Secondary structure predictions (mFOLD) of the recovered sequences revealed relatively stable stem-loop structures that resembled SL1, although the nucleotide sequences therein were different. Moreover, many of the clones selected in the fourth round conserved the TL and C-C mismatch, which suggests the importance of these elements in host protein binding. The SELEX clone that closely resembled the wt SL1 structure with the TL and C-C mismatch was able to replicate and cause systemic symptoms in plants, while most of the other winners replicated poorly only on inoculated leaves. The RNA replication level on protoplasts was also similarly affected. Taken together, these results indicate that the SL1 of PVX interacts with host protein(s) that play important roles related to virus replication.

• Journal of Ginseng Research
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• v.45 no.1
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• pp.86-97
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• 2021

Background: Panax ginseng Meyer has been used as a nourishing edible herb in East Asia for thousands of years. 25-OH-PPT was first discovered as a natural rare triterpenoid saponin in ginseng stems and leaves by our group. Research found that it showed strong inhibitory effects on α-glucosidase and protein tyrosine phosphatase 1B, and protected cardiocytes (H9c2) through PI3K/Akt pathway. Methods: In the research, in order to optimize the 25-OH-PPT enrichment process, optimal macroporous resins and optimal purification conditions were studied. Meanwhile, the hypoglycemic effect and mechanism of 25-OH-PPT were evaluated by using STZ to establish insulin-dependent diabetic mice and the spontaneous type 2 diabetes DB/DB mice. Results and Conclusion: Research found that 25-OH-PPT can reduce blood glucose and enhance glucose tolerance in STZ model mice. It increases insulin sensitivity by upregulating GLUT4 and AMPK in skeletal muscle, and activating insulin signaling pathways. In DB/DB mice, 25-OH-PPT achieves hypoglycemic effects mainly by activating the insulin signaling pathway. Meanwhile, through the influence of liver inflammatory factors and lipids in serum, it can be seen that 25-OH-PPT has obvious anti-inflammatory and lipid-lowering effects. These results provide new insights into the study of ginseng as a functional food.

• Molecules and Cells
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• v.43 no.12
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• pp.1011-1022
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• 2020

Cell type specification is a delicate biological event in which every step is under tight regulation. From a molecular point of view, cell fate commitment begins with chromatin alteration, which kickstarts lineage-determining factors to initiate a series of genes required for cell specification. Several important neuronal differentiation factors have been identified from ectopic over-expression studies. However, there is scarce information on which DNA regions are modified during induced pluripotent stem cell (iPSC) to neuronal progenitor cell (NPC) differentiation, the cis regulatory factors that attach to these accessible regions, or the genes that are initially expressed. In this study, we identified the DNA accessible regions of iPSCs and NPCs via the Assay for Transposase-Accessible Chromatin sequencing (ATAC-seq). We identified which chromatin regions were modified after neuronal differentiation and found that the enhancer regions had more active histone modification changes than the promoters. Through motif enrichment analysis, we found that NEUROD1 controls iPSC differentiation to NPC by binding to the accessible regions of enhancers in cooperation with other factors such as the Hox proteins. Finally, by using Hi-C data, we categorized the genes that directly interacted with the enhancers under the control of NEUROD1 during iPSC to NPC differentiation.

• Korean Journal of Metals and Materials
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• v.46 no.7
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• pp.427-436
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• 2008

The effect of dewpoints on annealing behavior and coating characteristics such as wettability and galvannealing kinetics was studied by annealing 0.3wt%Si - 0.1~0.4wt% Mn added interstitial-free high strength steels(IF-HSS). The 0.3wt%Si-0.1wt%Mn steel exhibited good wettability with molten zinc and galvannealing kinetics after annealing when the dewpoint of $H_2-N_2$ mixed gas was above $-20^{\circ}C$. It is shown that the wettability and galvannealing kinetics are directly related to the coverage of the external(surface) oxide formed by selective oxidation during annealing. At $N_2-15%H_2$ annealing atmosphere, the increase of dewpoint results in a gradual transition from external to internal selective oxidation. The decrease of external oxidation of alloying elements with a concurrent increase of their subsurface enrichment in the substrate, showing a larger surface area that was free of oxide particles, contributed to the improved wettability and galvannealing kinetics. On the other hand, the corresponding wettability and galvannealing kinetics were deteriorated with the dewpoints below $-20^{\circ}C$. The continuous oxide layer of network and/or film type was formed on the steel surface, leading to the poor wettability and galvannealing kinetics. It causes a high contact angle between annealed surface and molten zinc and plays an interrupting role in interdiffusion of Zn and Fe during galvannealing process.

• Corrosion Science and Technology
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• v.20 no.3
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• pp.158-168
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• 2021

Austenitic 316 stainless steel was irradiated with protons accelerated by an energy of 2 MeV at 360 ℃, the various defects induced by this proton irradiation were characterized with microscopic equipment. In our observations irradiation defects such as dislocations and micro-voids were clearly revealed. The typical irradiation defects observed differed according to depth, indicating the evolution of irradiation defects follows the characteristics of radiation damage profiles that depend on depth. Surface oxidation tests were conducted under the simulated primary water conditions of a pressurized water reactor (PWR) to understand the role irradiation defects play in surface oxidation behavior and also to investigate the resultant irradiation assisted stress corrosion cracking (IASCC) susceptibility that occurs after exposure to PWR primary water. We found that Cr and Fe became depleted while Ni was enriched at the grain boundary beneath the surface oxidation layer both in the non-irradiated and proton-irradiated specimens. However, the degree of Cr/Fe depletion and Ni enrichment was much higher in the proton-irradiated sample than in the non-irradiated one owing to radiation-induced segregation and the irradiation defects. The microstructural and microchemical changes induced by proton irradiation all appear to significantly increase the susceptibility of austenitic 316 stainless steel to IASCC.

• Molecules and Cells
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• v.45 no.5
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• pp.306-316
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• 2022

Chronic stress contributes to the risk of developing depression; the habenula, a nucleus in epithalamus, is associated with many neuropsychiatric disorders. Using genome-wide gene expression analysis, we analyzed the transcriptome of the habenula in rats exposed to chronic restraint stress for 14 days. We identified 379 differentially expressed genes (DEGs) that were affected by chronic stress. These genes were enriched in neuroactive ligand-receptor interaction, the cAMP (cyclic adenosine monophosphate) signaling pathway, circadian entrainment, and synaptic signaling from the Kyoto Encyclopedia of Genes and Genomes pathway analysis and responded to corticosteroids, positive regulation of lipid transport, anterograde trans-synaptic signaling, and chemical synapse transmission from the Gene Ontology analysis. Based on protein-protein interaction network analysis of the DEGs, we identified neuroactive ligand-receptor interactions, circadian entrainment, and cholinergic synapse-related subclusters. Additionally, cell type and habenular regional expression of DEGs, evaluated using a recently published single-cell RNA sequencing study (GSE137478), strongly suggest that DEGs related to neuroactive ligand-receptor interaction and trans-synaptic signaling are highly enriched in medial habenular neurons. Taken together, our findings provide a valuable set of molecular targets that may play important roles in mediating the habenular response to stress and the onset of chronic stress-induced depressive behaviors.

• Journal of Microbiology and Biotechnology
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• v.32 no.10
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• pp.1262-1274
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• 2022

Cholangiocarcinoma (CCA) is a complex and refractor type of cancer with global prevalence. Several barriers remain in CCA diagnosis, treatment, and prognosis. Therefore, exploring more biomarkers and therapeutic drugs for CCA management is necessary. CCA gene expression data was downloaded from the TCGA and GEO databases. KEGG enrichment, GO analysis, and protein-protein interaction network were used for hub gene identification. miRNA were predicted using Targetscan and validated according to several GEO databases. The relative RNA and miRNA expression levels and prognostic information were obtained from the GEPIA. The candidate drug was screened using pharmacophore-based virtual screening and validated by molecular modeling and through several in vitro studies. 301 differentially expressed genes (DEGs) were screened out. Complement and coagulation cascades-related genes (including AHSG, F2, TTR, and KNG1), and cell cycle-related genes (including CDK1, CCNB1, and KIAA0101) were considered as the hub genes in CCA progression. AHSG, F2, TTR, and KNG1 were found to be significantly decreased and the eight predicted miRNA targeting AHSG, F2, and TTR were increased in CCA patients. CDK1, CCNB1, and KIAA0101 were found to be significantly abundant in CCA patients. In addition, Molport-003-703-800, which is a compound that is derived from pharmacophores-based virtual screening, could directly bind to CDK1 and exhibited anti-tumor activity in cholangiocarcinoma cells. AHSG, F2, TTR, and KNG1 could be novel biomarkers for CCA. Molport-003-703-800 targets CDK1 and work as potential cell cycle inhibitors, thereby having potential for consideration for new chemotherapeutics for CCA.

• Food Science of Animal Resources
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• v.42 no.6
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• pp.1061-1073
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• 2022

Receptor activator of NF-kB ligand (RANKL) is known to play a major role in bone metabolism and the immune system, and its recombinant form has been expressed in bacterial systems for research since the last two decades. However, most of these recombinant forms are used after purification or directly using living cells. Here, there were cell extracts of recombinant Lactococcus lactis expressing mouse RANKL (mRANKL) used to evaluate its biological activity in mice. Mice were divided into three groups that were fed phosphate-buffered saline (PBS), wild-type L. lactis IL1403 (WT_CE), and recombinant L. lactis expressing mRANKL (mRANKL_CE). The small intestinal transcriptome and fecal microbiome were then profiled. The biological activity of mRANKL_CE was confirmed by studying RANK-RANKL signaling in vitro and in vivo. For small intestinal transcriptome, differentially expressed genes (DEGs) were identified in the mRANKL_CE group, and no DEGs were found in the WT_CE group. In the PBS vs. mRANKL_CE gene enrichment analysis, upregulated genes were enriched for heat shock protein binding, regulation of bone resorption, and calcium ion binding. In the gut microbiome analysis, there were no critical changes among the three groups. However, Lactobacillus and Sphingomonas were more abundant in the mRANKL_CE group than in the other two groups. Our results indicate that cell extracts of mRANKL_CE can play an effective role without a significant impact on the intestine. This strategy may be useful for the development of protein drugs.

• Journal of Veterinary Science
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• v.24 no.1
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• pp.13.1-13.11
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• 2023

Background: Highly pathogenic avian influenza viruses (HPAIVs) is an extremely contagious and high mortality rates in chickens resulting in substantial economic impact on the poultry sector. Therefore, it is necessary to elucidate the pathogenic mechanism of HPAIV for infection control. Objective: Gene set enrichment analysis (GSEA) can effectively avoid the limitations of subjective screening for differential gene expression. Therefore, we performed GSEA to compare HPAI-infected resistant and susceptible Ri chicken lines. Methods: The Ri chickens Mx(A)/BF2(B21) were chosen as resistant, and the chickens Mx(G)/BF2(B13) were selected as susceptible by genotyping the Mx and BF2 genes. The tracheal tissues of HPAIV H5N1 infected chickens were collected for RNA sequencing followed by GSEA analysis to define gene subsets to elucidate the sequencing results. Results: We identified four differentially expressed pathways, which were immune-related pathways with a total of 78 genes. The expression levels of cytokines (IL-1β, IL-6, IL-12), chemokines (CCL4 and CCL5), type interferons and their receptors (IFN-β, IFNAR1, IFNAR2, and IFNGR1), Jak-STAT signaling pathway genes (STAT1, STAT2, and JAK1), MHC class I and II and their co-stimulatory molecules (CD80, CD86, CD40, DMB2, BLB2, and B2M), and interferon stimulated genes (EIF2AK2 and EIF2AK1) in resistant chickens were higher than those in susceptible chickens. Conclusions: Resistant Ri chickens exhibit a stronger antiviral response to HPAIV H5N1 compared with susceptible chickens. Our findings provide insights into the immune responses of genetically disparate chickens against HPAIV.

• Economic and Environmental Geology
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• v.56 no.3
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• pp.259-275
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• 2023

Pan African granitoids of Kaiama is comprised of K-feldspar rich granites, porphyritic granites, and granitic gneiss that are intruded by quartz veins and aplitic veins and dykes which trend NE-SW. In order to establish the geochemical signatures, petrogenesis, and tectonic settings of the lithological units, petrological, petrographical, and geochemical studies was carried out. Petrographic analysis reveals that the granitoids are dominantly composed of quartz, plagioclase feldspar, biotite, and k-feldspar with occasional muscovites, sericite, and opaque minerals that constitute very low proportion. Major, trace, and rare earth elements geochemical data reveal that the rocks have moderate to high silica (SiO₂=63-79.7%) and alumina (Al₂O₃=11.85-16.15) contents that correlate with the abundance of quartz, feldspars, and biotite. The rocks are calc-alkaline, peraluminous (ASI=1.0-<1.2), and S-type granitoids sourced by melting of pre-existing metasedimentary or sedimentary rocks containing Al, Na, and K oxides. They plot dominantly in the WPG and VAG fields suggesting emplacement in a post-collisional tectonic setting. On a multi-element variation diagram, the granitoids show depletion in Ba, K, P, Rb, and Ti while enrichment was observed for Th, U, Nd, Pb and Sm. Their rare-earth elements pattern is characterized by moderate fractionation ((La/Yb)_N=0.52-38.24) and pronounced negative Eu-anomaly (Eu/Eu^*=0.02-1.22) that points to the preservation of plagioclase from the source magma. Generally, the geochemical features of the granitoids show that they were derived by the partial melting of crustal rocks with some input from greywacke and pelitic materials in a typical post-collisional tectonic setting.