• Molecules and Cells
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• 제42권5호
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• pp.418-425
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• 2019

Multicistronic elements, such as the internal ribosome entry site (IRES) and 2A-like cleavage sequence, serve crucial roles in the eukaryotic ectopic expression of exogenous genes. For utilization of multicistronic elements, the cleavage efficiency and order of elements in multicistronic vectors have been investigated; however, the dynamics of multicistronic element-mediated expression remains unclear. Here, we investigated the dynamics of encephalomyocarditis virus (EMCV) IRES- and porcine teschovirus-1 2A (p2A)-mediated expression. By utilizing real-time fluorescent imaging at a minute-level resolution, we monitored the expression of fluorescent reporters bridged by either EMCV IRES or p2A in two independent cultured cell lines, HEK293 and Neuro2a. We observed significant correlations for the two fluorescent reporters in both multicistronic elements, with a higher correlation coefficient for p2A in HEK293 but similar coefficients for IRES-mediated expression and p2A-mediated expression in Neuro2a. We further analyzed the causal relationship of multicistronic elements by convergent cross mapping (CCM). CCM revealed that in all four conditions examined, the expression of the preceding gene causally affected the dynamics of the subsequent gene. As with the cross correlation, the predictive skill of p2A was higher than that of IRES in HEK293, while the predictive skills of the two multicistronic elements were indistinguishable in Neuro2a. To summarize, we report a significant temporal correlation in both EMCV IRES- and p2A-mediated expression based on the simple bicistronic vector and real-time fluorescent monitoring. The current system also provides a valuable platform to examine the dynamic aspects of expression mediated by diverse multicistronic elements under various physiological conditions.

• Journal of the Computational Structural Engineering Institute of Korea
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• 제34권2호
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• pp.71-75
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• 2021

Despite the development of computational resources, the need to analyze models is increasing. The size of model has been increased to analyze the entire structure more accurately and precisely. As the analysis model becomes larger and more complex, the computation time increases exponentially. Various industries use many structures that have repeated patterns. We focus on these structures with repeated patterns and propose a dynamic analysis method to efficiently calculate these repeated structures. To devise an efficient method for repeated structures, the substructuring scheme and the degree of freedom-based reduction method are used in this study. We modify the existing reduction method in consideration of the characteristics of the repeating structure. In the proposed method, the entire structure was expressed as a combination of substructures, where each substructure was represented as an unit cell of repeated structures. The substructures were condensed and assembled using the substructuring scheme and the modified condensation method. Finally, numerical examples were demonstrated to verify the efficiency and accuracy of proposed method.

• Korean Journal of Agricultural Science
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• 제50권4호
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• pp.773-784
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• 2023

In this study, we developed a dynamic model and steering controller model for an autonomous tractor and evaluated their performance. The traction force was measured using a 6-component load cell, and the rotational speed of the wheels was monitored using proximity sensors installed on the axles. Torque sensors were employed to measure the axle torque. The PI (proportional integral) controller's coefficients were determined using the trial-error method. The coefficient of the P varied in the range of 0.1 - 0.5 and the I coefficient was determined in 3 increments of 0.01, 0.05, and 0.1. To validate the simulation model, we conducted RMS (root mean square) comparisons between the measured data of axle torque and the simulation results. The performance of the steering controller model was evaluated by analyzing the damping ratio calculated with the first and second overshoots. The average front and rear axle torque ranged from 3.29 - 3.44 and 6.98 - 7.41 kNm, respectively. The average rotational speed of the wheel ranged from 29.21 - 30.55 rpm at the front, and from 21.46 - 21.63 rpm at the rear. The steering controller model exhibited the most stable control performance when the coefficients of P and I were set at 0.5 and 0.01, respectively. The RMS analysis of the axle torque results indicated that the left and right wheel errors were approximately 1.52% and 2.61% (at front) and 7.45% and 7.28% (at rear), respectively.

• Animal Bioscience
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• 제37권2_spc호
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• pp.337-345
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• 2024

Ruminants possess a specialized four-compartment forestomach, consisting of the reticulum, rumen, omasum, and abomasum. The rumen, the primary fermentative chamber, harbours a dynamic ecosystem comprising bacteria, protozoa, fungi, archaea, and bacteriophages. These microorganisms engage in diverse ecological interactions within the rumen microbiome, primarily benefiting the host animal by deriving energy from plant material breakdown. These interactions encompass symbiosis, such as mutualism and commensalism, as well as parasitism, predation, and competition. These ecological interactions are dependent on many factors, including the production of diverse molecules, such as those involved in quorum sensing (QS). QS is a density-dependent signalling mechanism involving the release of autoinducer (AIs) compounds, when cell density increases AIs bind to receptors causing the altered expression of certain genes. These AIs are classified as mainly being N-acyl-homoserine lactones (AHL; commonly used by Gram-negative bacteria) or autoinducer-2 based systems (AI-2; used by Gram-positive and Gram-negative bacteria); although other less common AI systems exist. Most of our understanding of QS at a gene-level comes from pure culture in vitro studies using bacterial pathogens, with much being unknown on a commensal bacterial and ecosystem level, especially in the context of the rumen microbiome. A small number of studies have explored QS in the rumen using 'omic' technologies, revealing a prevalence of AI-2 QS systems among rumen bacteria. Nevertheless, the implications of these signalling systems on gene regulation, rumen ecology, and ruminant characteristics are largely uncharted territory. Metatranscriptome data tracking the colonization of perennial ryegrass by rumen microbes suggest that these chemicals may influence transitions in bacterial diversity during colonization. The likelihood of undiscovered chemicals within the rumen microbial arsenal is high, with the identified chemicals representing only the tip of the iceberg. A comprehensive grasp of rumen microbial chemical signalling is crucial for addressing the challenges of food security and climate targets.

• Biomolecules & Therapeutics
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• 제32권3호
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• pp.390-398
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• 2024

FoxO1, a member of the Forkhead transcription factor family subgroup O (FoxO), is expressed in a range of cell types and is crucial for various pathophysiological processes, such as apoptosis and inflammation. While FoxO1's roles in multiple diseases have been recognized, the target has remained largely unexplored due to the absence of cost-effective and efficient inhibitors. Therefore, there is a need for natural FoxO1 inhibitors with minimal adverse effects. In this study, docking, MMGBSA, and ADMET analyses were performed to identify natural compounds that exhibit strong binding affinity to FoxO1. The top candidates were then subjected to molecular dynamics (MD) simulations. A natural product library was screened for interaction with FoxO1 (PDB ID-3CO6) using the Glide module of the Schrödinger suite. In silico ADMET profiling was conducted using SwissADME and pkCSM web servers. Binding free energies of the selected compounds were assessed with the Prime-MMGBSA module, while the dynamics of the top hits were analyzed using the Desmond module of the Schrödinger suite. Several natural products demonstrated high docking scores with FoxO1, indicating their potential as FoxO1 inhibitors. Specifically, the docking scores of neochlorogenic acid and fraxin were both below -6.0. These compounds also exhibit favorable drug-like properties, and a 25 ns MD study revealed a stable interaction between fraxin and FoxO1. Our findings highlight the potential of various natural products, particularly fraxin, as effective FoxO1 inhibitors with strong binding affinity, dynamic stability, and suitable ADMET profiles.

• Journal of Microbiology and Biotechnology
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• 제34권3호
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• pp.663-672
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• 2024

The use of nanoparticles as a delivery system for a specific antigen could solve many limitations of mucosal vaccine applications, such as low immunogenicity, or antigen protection and stabilization. In this study, we tested the ability of nasally administered chitosan nanoparticles loaded with glycoprotein B of murine cytomegalovirus to induce an immune response in an animal model. The choice of chitosan nanoparticle type was made by in vitro evaluation of sorption efficiency and antigen release. Three types of chitosan nanoparticles were prepared: crosslinked with tripolyphosphate, coated with hyaluronic acid, and in complex with polycaprolactone. The hydrodynamic size of the nanoparticles by dynamic light scattering, zeta potential, Fourier transform infrared spectroscopy, scanning electron microscopy, stability, loading efficiency, and release kinetics with ovalbumin were evaluated. Balb/c mice were immunized intranasally using the three-dose protocol with nanoparticles, gB, and adjuvants Poly(I:C) and CpG ODN. Subsequently, the humoral and cell-mediated antigen-specific immune response was determined. On the basis of the properties of the tested nanoparticles, the cross-linked nanoparticles were considered optimal for further investigation. The results show that nanoparticles with Poly(I:C) and with gB alone raised IgG antibody levels above the negative control. In the case of mucosal IgA, only gB alone weakly induced the production of IgA antibodies compared to saline-immunized mice. The number of activated cells increased slightly in mice immunized with nanoparticles and gB compared to those immunized with gB alone or to negative control. The results demonstrated that chitosan nanoparticles could have potential in the development of mucosal vaccines.

• Radiation Oncology Journal
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• 제20권1호
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• pp.34-40
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• 2002

Purpose : This study was undertaken to retrospectively evaluate white blood ceil kinetics, especially lymphocyte depression after different treatments, and to find the correlation between immunosuppression and large blood volume and dynamic blood flow within the mediastinal radiotherapy (RT) field in lung cancer. Materials and Methods : Thirty-four patients with lung cancer were retrospectively evaluated; 10 patients had only radiotherapy (RT group), 8 had chemotherapy (CT group) and 16 fad chemotherapy and radio-therapy (RT/CT group). The mean follow-up periods of the RT-including groups (RT group and RT/CT group) and the RT-excluding group (CT group) were 6 and 8 months, respectively. Complete blood cell counts including lymphocyte percentage $(\%)$ were checked weekly during RT but less frequently during CT and after RT and after RT. Results : Changes in total white blood cell counts were not significantly different among the three groups. The lymphocyte count and lymphocyte $\%$ were much lower in the RT-including groups than in the RT-excluding group. The difference between pre-treatment and final lymphocyte count and the difference between pre-treatment and final lymphocyte $\%$ were significant (p=0.044 and p=0.037) between the RT-including groups and the RT-excluding group. Conclusion : lymphopenia was more marked after treatment containing RT than CT only. Lymphopenia may be one cause of a compromised immune system after mediastinal irradiation in lung cancer. We suggest cautiously that previous studies showing evidence of lymphocyte apoptosis after low-dose irradiation and large blood volume and dynamic blood flow within the RT fields could be somewhat related to lymphopenia after mediastinal irradiation.

• Journal of the Korea Academia-Industrial cooperation Society
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• 제19권1호
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• pp.537-545
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• 2018

In this study, transcriptome analysis was conducted to collect various information from Fagopyrum esculentum and Fagopyrum tataricum during the early germination stage. Total RNA was extracted from the seeds and at 12, 24, and 36 hrs after germination of Jeju native Fagopyrum esculentum and Fagopyrum tataricum and sequenced using the Illumina Hiseq 2000 platform. Raw data analysis was conducted using the Dynamic Trim and Lengths ORT programs in the SolexaQA package, and assembly and annotation were performed. Based on RNA-seq raw data, we obtained 16.5 Gb and 16.2 Gb of transcriptome data corresponding to about 84.2% and 81.5% of raw data, respectively. De novo assembly and annotation revealed 43,494 representative transcripts corresponding to 47.5Mb. Among them, 23,165 sequences were shown to have similar sequences with annotation DB. Moreover, Gene Ontology (GO) analysis of buckwheat representative transcripts confirmed that the gene is involved in metabolic processes (49.49%) of biological processes, as well as cell function (46.12%) in metabolic process, and catalytic activity (80.43%) in molecular function In the case of gibberellin receptor GID1C, which is related to germination of seeds, the expression levels increased with time after germination in both F. esculentum and F. tataricum. The expression levels of gibberellin 20-oxidase 1 were increased within 12 hrs of gemination in F. esculentum but continuously until 36 hrs in F. tataricum. This buckwheat transcriptome profile analysis of the early germination stage will help to identify the mechanism causing functional and morphological differences between species.

• Journal of the Korean Society of Food Science and Nutrition
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• 제34권1호
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• pp.13-20
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• 2005

The effects of pectin on obesity was studied using 3T3-L1 pre-adipocytes and rats fed 20% high fat diets. The concentration of leptin released from 3T3-L1 adipocytes in the presence of pectin was significantly decreased by 85% compared to that of the control (p<0.05), however, glycerol concentration was not changed. These data indicate that pectin seems to inhibit lipids accumulation in the adipocytes rather than enhance the lipolytic activity. Forty Sprague Dawley rats were fed 20% high fat diet for 8 weeks to induce obesity and then divided equally into four groups. Experimental groups were normal diet group (ND), high fat diet group (HFD), HDF with 10% pectin group (HFP10), and HDF with 20% pectin group (HFP20). Diet for the each group was prepared to be iso-caloric following AIN-76 guideline. After obesity was induced, rats were placed on an restricted diet for 9 weeks. The body weight of HFD increased 50% (p<0.05) compared to the ND, while it was decreased by 12% and 16% for HFP10 and HFP20, respectively (p<0.05). The relative amount of visceral fats for HFDl0 and HFD20 were decreased by 45% and 59% compared to that of HDF (130%), respectively (p<0.05). Pectin seems to have a greater effect on reducing visceral fats accumulation than weight reduction. Significantly increased level of triglyceride, total cholesterol or LDL-cholesterol in the plasma of HFD was returned to the normal or even below the normal by pectin diet, while the level of HDL-cholesterol increased. Lipid lowering effect was also observed in the liver and heart. These effects of pectin were dosedependent. In conclusion, the beneficial effect of pectin on the obesity was observed from cell culture experiment and animal study in terms of inhibiting the accumulation of lipids in the adipocytes.

• International Journal of Highway Engineering
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• 제10권1호
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• pp.87-95
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• 2008

One way to shield an atypical structure to secure the occupant safety of an impact vehicle is to stack energy absorbing material modules around the structure. To be applicable to a cushion module, material must have enough energy absorbing capabilities while satisfying the safety requirements of the vehicle occupant. Static compression test of the potential materials gives a good indication which material is good for a slacking module. This paper presents the mechanical properties that a cushion material must have to satisfy the safety requirements. Static tests are performed for Quard-Guard system module, sand bag, recycled tires, Geo-Container, Geo-Cell and Expanded Polystyren (EPS) Blocks. Static test results are discussed and EPS block of $30kg/m^{3}$ density showed good potential for a cushion module. To check the dynamic effect of EPS block, drop tests have been made up to 35.6km/h impact speed. Drop test results are compared with static test results and no appreciable difference was found. To improve the EPS module property, making holes to the block is suggested and drop test are performed for the modified blocks. From the drop test results, design values are suggested.