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

• Journal of Family Relations
• /
• v.22 no.4
• /
• pp.81-105
• /
• 2018

Objective: The purpose of this study was to analyze how couples relationship education (CRE) programs in Korean scholarly journals have been developed since they first appeared in 1994. Method: We selected articles that were published in journals related to human ecology and that included information about how the authors developed CRE programs (premarital education, marriage education). Using coding schemes based on the theoretical frameworks of CRE, we quantitatively coded programs in four specific areas: (a) overall characteristics, (b) program planning, (c) program construction and implementation, and (d) program evaluation. Results: Although CRE programs have increased and evolved since the 1990s, the literature has been limited on testing long-term program efficacy, developing dissemination plans, and applying theories to program design. In terms of program participants and content, most programs had similar themes despite their differences in the target audience. We also found that few programs have been provided for diverse couples. As for evaluation, pre- and post-testing was the most common method of efficacy test. Conclusion: Our findings suggest that family researchers and practitioners develop more elaborate and systematic programs to advance CRE in Korea as a core topic of family life education and to provide evidence-informed practice.

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

• The Bulletin of The Korean Astronomical Society
• /
• v.45 no.1
• /
• pp.38.2-38.2
• /
• 2020

Horizon Run 5 (HR5) is a cosmological hydrodynamical simulation which captures the properties of the Universe on a Gpc scale while achieving a resolution of 1 kpc. This enormous dynamic range allows us to simultaneously capture the physics of the cosmic web on very large scales and account for the formation and evolution of dwarf galaxies on much smaller scales. Inside the simulation box. we zoom-in on a high-resolution cuboid region with a volume of 1049 × 114 × 114 Mpc3. The subgrid physics chosen to model galaxy formation includes radiative heating/cooling, reionization, star formation, supernova feedback, chemical evolution tracking the enrichment of oxygen and iron, the growth of supermassive black holes and feedback from active galactic nuclei (AGN) in the form of a dual jet-heating mode. For this simulation we implemented a hybrid MPI-OpenMP version of the RAMSES code, specifically targeted for modern many-core many thread parallel architectures. For the post-processing, we extended the Friends-of-Friend (FoF) algorithm and developed a new galaxy finder to analyse the large outputs of HR5. The simulation successfully reproduces many observations, such as the cosmic star formation history, connectivity of galaxy distribution and stellar mass functions. The simulation also indicates that hydrodynamical effects on small scales impact galaxy clustering up to very large scales near and beyond the baryonic acoustic oscillation (BAO) scale. Hence, caution should be taken when using that scale as a cosmic standard ruler: one needs to carefully understand the corresponding biases. The simulation is expected to be an invaluable asset for the interpretation of upcoming deep surveys of the Universe.

• Proceedings of the Korean Society of Crop Science Conference
• /
• 2022.10a
• /
• pp.229-229
• /
• 2022

Rapeseed is a crop that is waterlogging sensitive, and it is necessary to breed waterlogging tolerance varieties. Our study presents the comparative transcriptome changes in two rapeseed lines, i.e., waterlogging-tolerant (tJ8634-B-30,) and - sensitive ('EMS26') lines under control and waterlogging stress treatments at the flowering stage. RNA-sequencing analysis revealed 13,279 differentially expressed genes (DEGs) for 'J8634-B-30' and 8,682 DEGs for 'EMS26' under waterlogging stress condition compared to control. Among DEGs of 'J8634-B-30', 6,818 were up-regulated and 6,461 were down-regulated. On the other hand, among the DEGs of 'EMS26', the number of down-regulated genes (5,240) were higher than that of up-regulated genes (3,442). Gene ontology enrichment analysis showed that DEGs related to glucan metabolic, cell wall, and oxidoreductase activity were significantly changed in 'J8634-B-30'. Kyoto Encyclopedia of Genes and Genomes (KEGG)-based analysis in 'J8634-B-30' identified up-regulated DEGs being involved in MAPK signaling pathways. In addition, the DEGs belonging to mechanisms responding to waterlogging stress, i.e., plant hormones, carbon metabolism, Reactive oxygen species (ROS), Nitric oxide (NO) etc. were compared in rapeseed lines. Several DEGs including ethylene-responsive transcription factor (ERF), constitutive triple response (CTR) (in ethylene signaling pathway), monodehydroascorbate Reductase (MDAR), NADPH oxidase (in ROS pathway), cytochrome c oxidase assembly protein (COX) (in NO pathway) up-regulated in 'J8634-B-30'. These outcomes provided the valuable information for further exploring the genetic mechanism of waterlogging tolerance in rapeseed.

• Genomics & Informatics
• /
• v.21 no.3
• /
• pp.36.1-36.19
• /
• 2023

The LIM domain-containing proteins are dominantly found in plants and play a significant role in various biological processes such as gene transcription as well as actin cytoskeletal organization. Nevertheless, genome-wide identification as well as functional analysis of the LIM gene family have not yet been reported in the economically important plant sorghum (Sorghum bicolor L.). Therefore, we conducted an in silico identification and characterization of LIM genes in S. bicolor genome using integrated bioinformatics approaches. Based on phylogenetic tree analysis and conserved domain, we identified five LIM genes in S. bicolor (SbLIM) genome corresponding to Arabidopsis LIM (AtLIM) genes. The conserved domain, motif as well as gene structure analyses of the SbLIM gene family showed the similarity within the SbLIM and AtLIM members. The gene ontology (GO) enrichment study revealed that the candidate LIM genes are directly involved in cytoskeletal organization and various other important biological as well as molecular pathways. Some important families of regulating transcription factors such as ERF, MYB, WRKY, NAC, bZIP, C2H2, Dof, and G2-like were detected by analyzing their interaction network with identified SbLIM genes. The cis-acting regulatory elements related to predicted SbLIM genes were identified as responsive to light, hormones, stress, and other functions. The present study will provide valuable useful information about LIM genes in sorghum which would pave the way for the future study of functional pathways of candidate SbLIM genes as well as their regulatory factors in wet-lab experiments.

• Herbal Formula Science
• /
• v.31 no.4
• /
• pp.295-313
• /
• 2023

Objectives : While treatments for cancer are advancing, the development of effective treatments for cancer metastasis, the main cause of cancer patient death, remains insufficient. Recent studies on Dichroae Radix have revealed that its active ingredients have the potential to inhibit cancer metastasis. This study aimed to investigate the cancer metastasis inhibitory effect of Dichroae Radix using network pharmacological analysis. Methods : The active compounds of Dichroae Radix have been identified using Traditional Chinese Medicine System Pharmacology Database and Analysis Platform. The UniProt database was used to collect each of information of all target proteins associated with the active compounds. To find the bio-metabolic processes associated with each target, the DAVID6.8 Gene Functional classifier tool was used. Compound-Target and Target-Pathway networks were analyzed via Cytoscape 3.40. Results : In total, 25 active compounds and their 62 non-redundant targets were selected through the TCMSP database and analysis platform. The target genes underwent gene ontology and pathway enrichment analysis. The gene list applied to the gene ontology analysis revealed associations with various biological processes, including signal transduction, chemical synaptic transmission, G-protein-coupled receptor signaling pathways, response to xenobiotic stimulus, and response to drugs, among others. A total of eleven genes, including HSP90AB1, CALM1, F2, AR, PAKACA, PTGS2, NOS2, RXRA, ESR1, ESR2, and NCOA1, were found to be associated with biological pathways related to cancer metastasis. Furthermore, nineteen of the active compounds from Dichroae Radix were confirmed to interact with these genes. Conclusions : The results provide valuable insights into the mechanism of action and molecular targets of Dichroae Radix. Notably, Berberine, the main active ingredient of Dichroae Radix, plays a significant role in degrading AR proteins in advanced prostate cancer. Further studies and validations can provide crucial data to advance cancer metastasis prevention and treatment strategies.

• Journal of Bio-Environment Control
• /
• v.31 no.4
• /
• pp.485-496
• /
• 2022

Modern agriculture is being transformed into smart agriculture to maximize production efficiency along with changes in the 4th industrial revolution. However, rural areas in Korea are facing challenges of aging, low fertility, and population outflow, making it difficult to transition to smart agriculture. Among ICT technologies, simulation allows users to observe or experience the results of their choices through imitation or reproduction of reality. The combination of the three-dimension (3D) model and the greenhouse simulator enable a 3D experience by virtual greenhouse for fruits and vegetable cultivation. At the same time, it is possible to visualize the greenhouse under various cultivation or climate conditions. The objective of this study is to apply the greenhouse climate management model for simulation development that can visually see the state of the greenhouse environment under various micrometeorological properties. The numerical solution with the mathematical model provided a dynamic change in the greenhouse environment for a particular greenhouse design. Light intensity, crop transpiration, heating load, ventilation rate, the optimal amount of CO₂ enrichment, and daily light integral were calculated with the simulation. The results of this study are being built so that users can be linked through a web page, and software will be designed to reflect the characteristics of cladding materials and greenhouses, cultivation types, and the condition of environmental control facilities for customized environmental control. In addition, environmental information obtained from external meteorological data, as well as recommended standards and set points for each growth stage based on experiments and research, will be provided as optimal environmental factors. This simulation can help growers, students, and researchers to understand the ICT technologies and the changes in the greenhouse microclimate according to the growing conditions.

• Journal of The Korean Association For Science Education
• /
• v.20 no.1
• /
• pp.112-136
• /
• 2000

In this study, literatures concerning the scientifically gifted/talented were identified through exploration of ERIC(Education Research Information Center) and then categorized. Existing educational programs for the scientifically gifted/talented were analyzed to aid in development and progress of education program of the scientifically gifted/talented. The followings are the results of this study 1. Exploration of ERIC from 1981 to 1997 showed 150 documents related to the scientifically gifted/talented and of those found there were 63 scientifically gifted/talented education program documents which accounts for 42.0%. 2. 42.0% of documents related to the scientifically gifted/talented and 65.1% of education program for the scientifically gifted/talented were in the publication type of journal articles. 3. 60.0% of documents related to the scientifically gifted/talented and 68.3% of education program for the scientifically gifted/talented were in the type of paper of reports. 4. 71.4% of education programs for the gifted/talented was centered around scientifically gifted/talented students in middle or high school. 5. 52.4% of education programs for the scientifically gifted/talented was being carried out as an supplementary enrichment education program such as summer programs or short term projects. Education programs for the scientifically gifted/talented carried out as a regular class accounted for 38.1%. 6. Systems like Mentorship System and Internship System is being well carried out due to good interrelationships between universities and institutions. There were many programs encouraging majors and careers in science related fields. 7. Individualized education, which is effective in teaching the scientifically gifted/talented whose abilities, interests, and attitudes differ, is being well carried out.

• The Korean Journal of Quaternary Research
• /
• v.17 no.2
• /
• pp.165-165
• /
• 2003

A borehole core ECSDP-102 (about 68.5 m long) has been investigated to get information on paleoenvironmental changes in response to the sea-level fluctuations during the period of late Quaternary. Several AMS $\^$14/C ages show that the core ECSDP-102 recorded the depositional environments of the northern East China Sea for approximately 60 ka. The Yangtze River discharged huge amounts of sediment into the northern East China Sea during the marine isotope stage (MIS) 3. In particular, $\delta$$\^$13/Corg values reveal that the sedimentary environments of the northern East China Sea, which is similar to the Holocene conditions, have taken place three times during the MIS 3. It is supported by the relatively enriched $\delta$$\^$13/Corg values of -23 to -21$\textperthousand$ during the marine settings of MIS 3 that are characterized by the predominance of marine organic matter akin to the Holocene. Furthermore, we investigated the three Holocene sediment cores, ECSDP-101, ECSDP-101 and YMGR-102, taken from the northern East China Sea off the mouth of the Yangtze River and from the southern Yellow Sea, respectively. Our study was focused primarily on the onset of the post-glacial marine transgression and the reconstructing of paleoenvironmental changes in the East China Sea and the Yellow Sea during the Holocene. AMS $\^$14/C ages indicate that the northern East China Sea and the southern Yellow Sea began to have been flooded at about 13.2 ka BP which is in agreement with the initial marine transgression of the central Yellow Sea (core CC-02). $\delta$$\^$18/O and $\delta$$\^$13/C records of benthic foraminifera Ammonia ketienziensis and $\delta$$\^$13/Corg values provide information on paleoenvironmental changes from brackish (estuarine) to modem marine conditions caused by globally rapid sea-level rise since the last deglaciation. Termination 1 (T1) ended at about 9.0-8.7 ka BP in the southern and central Yellow Sea, whereas T1 lasted until about 6.8 ka BP in the northern East China Sea. This time lag between the two seas indicates that the timing of the post-glacial marine transgression seems to have been primarily influenced by the bathymetry. The present marine regimes in the northern East China Sea and the whole Yellow Sea have been contemporaneously established at about 6.0 ka BP. This is strongly supported by remarkably changes in occurrence of benthic foraminiferal assemblages, $\delta$$\^$18/O and $\delta$$\^$13/C compositions of A. ketienziensis, TOC content and $\delta$$\^$13/Corg values. The $\delta$$\^$18/O values of A. ketienziensis show a distinct shift to heavier values of about 1$\textperthousand$ from the northern East China Sea through the southern to central Yellow Sea. The northward shift of $\^$18/O enrichment may reflect gradually decrease of the bottom water temperature in the northern East China Sea and the Yellow Sea.