• Korean Journal of Agricultural and Forest Meteorology
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• v.12 no.2
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• pp.122-131
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• 2010

This paper introduces the concept of a virtual ecosystem and reports the following three mathematical approaches that could be widely used to construct such an ecosystem, along with examples: (1) a molecular dynamics simulation approach for animal flocking behavior, (2) a stochastic lattice model approach for termite colony behavior, and (3) a rule-based cellular automata approach for biofilm growth. The ecosystem considered in this study consists of artificial organisms and their environment. Each organism in the ecosystem is an agent that interacts autonomously with the dynamic environment, including the other organisms within it. The three types of model were successful to account for each corresponding ecosystem. In order to accurately mimic a natural ecosystem, a virtual ecosystem needs to take many ecological variables into account. However, doing so is likely to introduce excess complexity and nonlinearity in the analysis of the virtual ecosystem's dynamics. Nonetheless, the development of a virtual ecosystem is important, because it can provide possible explanations for various phenomena such as environmental disturbances and disasters, and can also give insights into ecological functions from an individual to a community level from a synthetic viewpoint. As an example of how lower and higher levels in an ecosystem can be connected, this paper also briefly discusses the application of the second model to the simulation of a termite ecosystem and the influence of climate change on the termite ecosystem.

• Biomolecules & Therapeutics
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• v.29 no.2
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• pp.234-247
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• 2021

We used a heterozygous gene deletion library of fission yeasts comprising all essential and non-essential genes for a microarray screening of target genes of the antifungal terbinafine, which inhibits ergosterol synthesis via the Erg1 enzyme. We identified 14 heterozygous strains corresponding to 10 non-essential [7 ribosomal-protein (RP) coding genes, spt7, spt20, and elp2] and 4 essential genes (tif302, rpl2501, rpl31, and erg1). Expectedly, their erg1 mRNA and protein levels had decreased compared to the control strain SP286. When we studied the action mechanism of the non-essential target genes using cognate haploid deletion strains, knockout of SAGA-subunit genes caused a down-regulation in erg1 transcription compared to the control strain ED668. However, knockout of RP genes conferred no susceptibility to ergosterol-targeting antifungals. Surprisingly, the RP genes participated in the erg1 transcription as components of repressor complexes as observed in a comparison analysis of the experimental ratio of erg1 mRNA. To understand the action mechanism of the interaction between the drug and the novel essential target genes, we performed isobologram assays with terbinafine and econazole (or cycloheximide). Terbinafine susceptibility of the tif302 heterozygous strain was attributed to both decreased erg1 mRNA levels and inhibition of translation. Moreover, Tif302 was required for efficacy of both terbinafine and cycloheximide. Based on a molecular modeling analysis, terbinafine could directly bind to Tif302 in yeasts, suggesting Tif302 as a potential off-target of terbinafine. In conclusion, this genome-wide screening system can be harnessed for the identification and characterization of target genes under any condition of interest.

• BMB Reports
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• v.55 no.9
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• pp.453-458
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• 2022

Diabetes mellitus (DM) is a serious disease in which blood sugar levels rise abnormally because of failed insulin production or decreased insulin sensitivity. Although many studies are being conducted for the treatment or early diagnosis of DM, it is not fully understood how mitochondrial genome (mtDNA) abnormalities appear in patients with DM. Here, we induced iPSCs from fibroblasts, PBMCs, or pancreatic cells of three patients with type 2 DM (T2D) and three patients with non-diabetes counterpart. The mtDNA mutations were detected randomly without any tendency among tissues or patients. In T2D patients, 62% (21/34) of iPSC clones harbored multiple mtDNA mutations, of which 37% were homoplasmy at the 100% mutation level compared to only 8% in non-diabetes. We next selected iPSC clones that were a wild type or carried mutations and differentiated into pancreatic cells. Oxygen consumption rates were significantly lower in cells carrying mutant mtDNA. Additionally, the mutant cells exhibited decreased production of insulin and reduced secretion of insulin in response to glucose. Overall, the results suggest that screening mtDNA mutations in iPSCs from patients with T2D is an essential step before pancreatic cell differentiation for disease modeling or autologous cell therapy.

• Clean Technology
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• v.28 no.3
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• pp.210-217
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• 2022

Boron(B) is a rare resource used for various purposes such as glass, semiconductor materials, gunpowder, rocket fuel, etc. However, Korea depends entirely on imports for boron. Considering the global boron reserves and its current production rate, boron will be depleted on earth in 50 years. Thus, a process including proper adsorbent materials recovering boron from seawater is demanded. This research proposed carbonized nanofibers prepared from electrospun PAN(polyacrylonitrile) mats as promising materials to adsorb boron in aqueous solution. First, the mechanism of boron adsorption on carbonized nanofibers was investigated by DFT(density functional method)-based molecular modeling and the calculated energetics demonstrated that the boron chemisorption on the nitrogen-doped graphene surface by a two-step dehydration is possible with viable activation energies. Then, the electrospun PAN mats were stabilized in air and then carbonized in an argon atmosphere before being immersed in the boric acid aqueous solution. Analytically, SEM(scanning electron microscopy) and Raman measurements were employed to confirm whether the electrospinning and carbonization of PAN mats proceeded successfully. Then, XPS(X-ray photoelectron spectroscopy) peak analysis showed whether the intended nitrogen-doped carbon nanofiber surface was formed and boron was properly adsorbed on nanofibers. Those results demonstrated that the carbonized nanofibers prepared from electrospun PAN mats could be feasible adsorbents for boron recovery in seawater.

• Nuclear Medicine and Molecular Imaging
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• v.42 no.4
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• pp.275-284
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• 2008

Purpose: We intended to evaluate myocardial oxygen consumption ($MVO_2)$ by applying recirculation correction and modified one-compartment model to have a reference range of $MVO_2$ in normal young population and to reveal the effect of recirculation on time-activity curve (TAC). Materials and Methods: In nine normal male volunteers with mean age of $26.3{\pm}4.0$, $MVO_2$ was estimated with 925 MBq (25mCi) of $^{11}C$-Acetate (Neuroscience Research Institute, Gachon University of Medicine and Science, Incheon, Korea) and PET/CT (Biograph 6, Siemens Medical Solution, Germany). Analysis software such as $MATLAB^{(R)}$ v7.1 (Mathworks, Inc., United States), $Excel^{(R)}$ 2007 (Microsoft, United States), and $SPSS^{(R)}$ v12.0 (Apache Software Foundation, United States) were used. Twenty three frames were of $12{\times}10$, $5{\times}60$, $3{\times}120$, $2{\times}300's$ duration, respectively. The modified one-compartmental model and the recirculation correction method were applied. Statistical analysis was performed by using Test of Normality, ANOVA and Post-Hoc (Scheffe's) analysis, and p-value less than 0.05 was considered as significant. Results: The normal reference ranges of $MVO_2$ were presented as $3.18-4.64\;{\times}\;10^{-4}\;ml/g/sec$, $1.91-3.94\;{\times}\;10^{-4}\;ml/g/sec$, $4.31-6.40\;{\times}\;10^{-4}\;ml/g/sec$, $2.84-4.53\;{\times}\;10^{-4}\;ml/g/sec$ and $3.42-5.00\;{\times}\;10^{-4}\;ml/g/sec$ in the septum, the inferior wall, the lateral wall, the anterior wall and the entire wall, respectively. In addition, it was noted that the dual exponentiality of the clearance curve is due to the recirculation effect and that the characteristic of the curve is essentially mono-exponential. Conclusion: $^{11}C$-Acetate is a radiotracer worthwhile to assess $MVO_2$. Re-circulated $^{11}C$ can influence TAC of $^{11}C$ in myocadia and so the recirculation correction must be considered when measuring $MVO_2$.

• Journal of The Korean Association For Science Education
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• v.34 no.5
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• pp.437-447
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• 2014

Learning progressions (LP), which describe how students may develop more sophisticated understanding over a defined period of time, can inform the design of instructional materials and assessment by providing a coherent, systematic measure of what can be regarded as "level appropriate." We developed LPs for the nature of matter for grades K-16. In order to empirically test Korean students, we revised one of the constructs and associated assessment items based on Korean National Science Standards. The assessment was administered to 124 Korean secondary students to measure their knowledge and submicroscopic representations, and to assign them to a level of learning progression for the particle nature of matter. We characterized the level of students' understanding and models of the particle nature of matter, and described how students interpret various representations of atoms and molecules to explain scientific phenomena. The results revealed that students have difficulties in understanding the relationship between the macroscopic and molecular levels of phenomena, even in high school science. Their difficulties may be attributed to a limited understanding of scientific modeling, a lack of understanding of the models used to represent the particle nature of matter, or limited understanding of the structure of matter. This work will inform assessment and curriculum materials development related to the fundamental relationship between macroscopic, observed phenomena and the behavior of atoms and molecules, and can be used to create individualized learning environments. In addition, the results contribute to scientific research literature on learning progressions on the nature of matter.

• Proceedings of the Korean Society of Near Infrared Spectroscopy Conference
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• 2001.06a
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• pp.1031-1031
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• 2001

The mammary gland is made up of remarkably sensitive tissue, which has the capability of producing a large volume of secretion, milk, under normal or healthy conditions. When bacteria enter the gland and establish an infection (mastitis), inflammation is initiated accompanied by an influx of white cells from the blood stream, by altered secretory function, and changes in the volume and composition of secretion. Cell numbers in milk are closely associated with inflammation and udder health. These somatic cell counts (SCC) are accepted as the international standard measurement of milk quality in dairy and for mastitis diagnosis. NIR Spectra of unhomogenized composite milk samples from 14 cows (healthy and mastitic), 7days after parturition and during the next 30 days of lactation were measured. Different multivariate analysis techniques were used to diagnose the disease at very early stage and determine how the spectral properties of milk vary with its composition and animal health. PLS model for prediction of somatic cell count (SCC) based on NIR milk spectra was made. The best accuracy of determination for the 1100-2500nm range was found using smoothed absorbance data and 10 PLS factors. The standard error of prediction for independent validation set of samples was 0.382, correlation coefficient 0.854 and the variation coefficient 7.63%. It has been found that SCC determination by NIR milk spectra was indirect and based on the related changes in milk composition. From the spectral changes, we learned that when mastitis occurred, the most significant factors that simultaneously influenced milk spectra were alteration of milk proteins and changes in ionic concentration of milk. It was consistent with the results we obtained further when applied 2DCOS. Two-dimensional correlation analysis of NIR milk spectra was done to assess the changes in milk composition, which occur when somatic cell count (SCC) levels vary. The synchronous correlation map revealed that when SCC increases, protein levels increase while water and lactose levels decrease. Results from the analysis of the asynchronous plot indicated that changes in water and fat absorptions occur before other milk components. In addition, the technique was used to assess the changes in milk during a period when SCC levels do not vary appreciably. Results indicated that milk components are in equilibrium and no appreciable change in a given component was seen with respect to another. This was found in both healthy and mastitic animals. However, milk components were found to vary with SCC content regardless of the range considered. This important finding demonstrates that 2-D correlation analysis may be used to track even subtle changes in milk composition in individual cows. To find out the right threshold for SCC when used for mastitis diagnosis at cow level, classification of milk samples was performed using soft independent modeling of class analogy (SIMCA) and different spectral data pretreatment. Two levels of SCC - 200 000 cells/$m\ell$ and 300 000 cells/$m\ell$, respectively, were set up and compared as thresholds to discriminate between healthy and mastitic cows. The best detection accuracy was found with 200 000 cells/$m\ell$ as threshold for mastitis and smoothed absorbance data: - 98% of the milk samples in the calibration set and 87% of the samples in the independent test set were correctly classified. When the spectral information was studied it was found that the successful mastitis diagnosis was based on reviling the spectral changes related to the corresponding changes in milk composition. NIRS combined with different ways of spectral data ruining can provide faster and nondestructive alternative to current methods for mastitis diagnosis and a new inside into disease understanding at molecular level.

• Microbiology and Biotechnology Letters
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• v.37 no.3
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• pp.248-257
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• 2009

The inhibitors against Vibrio harveyi quorum sensing (QS) signaling were developed by modifying the molecular structure of the major signal, N-3-hydroxybutanoyl-L-homoserine lactone (3-OH-$C_4$-HSL). A series of structural derivatives, N-(3-hydroxysulfonyl)-L-homoserine lactones (HSHLs) were synthesized by the solid-phase organic synthesis method. The in vivo QS inhibition by these compounds was measured by a bioassay system using the V. harveyi bioluminescence, and all showed significant inhibitory effects. To analyze the interaction between these compounds and LuxN, a 3-OH-$C_4$-HSL receptor protein of V. harveyi, we tentatively determined the putative signal binding domain of LuxN based on the sequence homology with other acyl-HSL binding proteins, and predicted the partial 3-D structure of the putative signal binding domain of LuxN by using ORCHESTRA program, and further estimated the binding poses and energies (docking scores) of 3-OH-$C_4$-HSL and HSHLs within the domain. In comparison of the result from this modeling study with that of in vivo bioassay, we suggest that the in silica interpretation of the interaction between ligands and their receptor proteins can be a valuable way to develop better competitive inhibitors, especially in the case that the structural information of the protein is limited.

• Nuclear Medicine and Molecular Imaging
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• v.41 no.4
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• pp.317-325
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• 2007

Purpose: Biological parameters can be quantified using dynamic PET data with compartment modeling and Nonlinear Least Square (NLS) estimation. However, the generation of parametric images using the NLS is not appropriate because of the initial value problem and excessive computation time. In irreversible model, Patlak graphical analysis (PGA) has been commonly used as an alternative to the NLS method. In PGA, however, the start time ($t^*$, time where linear phase starts) has to be determined. In this study, we suggest a new Multiple Linear Analysis for irreversible radiotracer (MLAIR) to estimate fluoride bone influx rate (Ki). Methods: $[^{18}F]Fluoride$ dynamic PET scans was acquired for 60 min in three normal mini-pigs. The plasma input curve was derived using blood sampling from the femoral artery. Tissue time-activity curves were measured by drawing region of interests (ROls) on the femur head, vertebra, and muscle. Parametric images of Ki were generated using MLAIR and PGA methods. Result: In ROI analysis, estimated Ki values using MLAIR and PGA method was slightly higher than those of NLS, but the results of MLAIR and PGA were equivalent. Patlak slopes (Ki) were changed with different $t^*$ in low uptake region. Compared with PGA, the quality of parametric image was considerably improved using new method. Conclusion: The results showed that the MLAIR was efficient and robust method for the generation of Ki parametric image from $[^{18}F]Fluoride$ PET. It will be also a good alternative to PGA for the radiotracers with irreversible three compartment model.

• Journal of Life Science
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• v.23 no.5
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• pp.609-615
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• 2013

Glyceollin I has gained attention as a useful therapy for various dermatological diseases. However, the binding property of glyceollin I to the mammalian adenylyl cyclase (hereafter mAC), a critical target enzyme for the down-regulation of skin melanogenesis, has not been fully explored. To clarify the action mechanism between glyceollin I and mAC, we first investigated the molecular docking property of glyceollin I to mAC and compared with that of SQ22,536, a well-known mAC inhibitor, to mAC. Glyceollin I showed superiority by forming three hydrogen bonds with Asp 1018, Trp 1020, and Asn 1025, which exist in the catalytic site of mAC. However, SQ22,536 formed only two hydrogen bonds with Asp 1018 and Asn 1025. Secondly, we confirmed that glyceollin I effectively inhibits the formation of forskolin-induced cAMP and the phosphorylation of PKA from a cell-based assay. Long term treatment with glyceollin I had little effect on the cell viability. The findings of the present study also suggest that glyceollin I may be extended to be used as an effective inhibitor of hyperpigmentation.