• Journal of the Korea Computer Graphics Society
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• v.23 no.4
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• pp.31-40
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• 2017

As 3D cell culture has recently become possible, it has been able to observe a 3D shape of cell and volume. Generally, 3D information of a cell should be observed with a special microscope such as a confocal microscope or an electron microscope. However, a confocal microscope is more expensive than a conventional microscope and takes longer time to capture images. Therefore, there is a need for a method that can reconstruct the 3D shape of cells using a common microscope. In this paper, we propose a method of reconstructing 3D cells using the focus estimator value from multi-focal fluorescence images of cells. Initially, 3D cultured cells are captured with an optical microscope by changing the focus. Then the approximate position of the cells is assigned as ROI (Region Of Interest) using the circular Hough transform in the images. The MSBF (Modified Sliding Band Filter) is applied to the obtained ROI to extract the outlines of the cell clusters, and the focus estimator values are computed based on the extracted outlines. Using the computed focus estimator values and the numerical aperture (NA) of the microscope, we extract the outline of the cell cluster considering the depth and reconstruct the cells into 3D based on the extracted outline. The reconstruction results are examined by comparing with the combined in-focus portions of the cell images.

• Microbiology and Biotechnology Letters
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• v.47 no.1
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• pp.164-171
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• 2019

Radiation therapy has many side effects, such as digestive mucosal ulcers, without regard to its efficacy. The purpose of this study is to address an alternative method to replace the limitation of radiation therapy using radiomimetic microbial ribotoxins. In the evaluation of cancer therapy, we analyzed the formation of colorectal cancer (CRC) cell spheroids, which can take into account the heterogeneous cellular constitution, tumor stem cells, and the surrounding microenvironment. Ribotoxic stress interfered with the spheroid structure composed of relatively small clusters. Spheroids under ribotoxic stress were structurally sparse and their shrinkage was very slow. In the control group, the clusters of strongly aggregated cells were resistant to physical stress, but the ribotoxic stress-exposed spheroids were easily broken up by the physical stress. Moreover, the ribosome-insulted CRC cells slowly migrated to form clusters and the cell-cell junctional points in the ribosome-insulted spheroids were rarer than those in the control CRC spheroid. Moreover, levels of the cell-to-cell junctional protein E-cadherin were suppressed by ribotoxic stress in both allograft and xenograft spheroids. In conclusion, the radiomimetic microbial ribotoxins induced structural defects in CRC cell spheroids via retardation of migration and cell-cell junction in the formation of three-dimensional structures, and provides a basis for the mechanism of pharmacological radiomimetic anticancer actions as an alternate to radiotherapy against cancer.

• Journal of the Korean Society of Visualization
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• v.18 no.2
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• pp.10-17
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• 2020

The curvature of wound boundaries has been identified as a key modulator that determines a type of force responsible for cell migration. While several studies report how certain curvatures of the boundary correlate with the rate at which the wound closes, it remains unclear how these curvatures are spatiotemporally formed to regulate the healing process. We investigated the dynamic changes in the boundary curvatures by visualizing cell migration patterns. Locally, cells at the convex boundary continuously move forward with transmitting kinetic responses behind to the cells away from the boundary, and cells at the concave boundary exhibit dramatic contracting motion, like a purse-string, when they accumulate enough negative curvatures to gain the thrust toward the void. Globally, the dynamics of boundary geometries are controlled by the diffusive flow of cells driven by the density gradient between the wound area and the cell layer.

• Journal of the Korean Society of Visualization
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• v.20 no.2
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• pp.70-77
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• 2022

Skeletal muscle tissues feature cellular heterogeneity, including differentiated myofibers, myoblasts, and satellite cells. Thanks to the presence of undifferentiated myoblasts and satellite cells, skeletal muscle tissues can self-regenerate after injury. In skeletal muscle regeneration, the collective motions among these cell types must play a significant role, but little is known about the dynamic collective behavior during the regeneration. In this study, we constructed in vitro platform to visualize the migration behavior of skeletal muscle cells in specific conditions that mimic the biochemical environment of injured skeletal muscles. We then visualized the spatiotemporal distribution of stresses arising from the differential collectiveness in the cellular clusters under different conditions. From these analyses, we identified that the heterogeneous population of muscle cells exhibited distinct collective migration patterns in the injury-mimicking condition, suggesting selective activation of a specific cell type by the biochemical cues from the injured skeletal muscles.

• The Korean Journal of Applied Statistics
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• v.32 no.3
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• pp.331-348
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• 2019

Understanding the tumor heterogeneity due to differences in the growth pattern of metastatic tumors and rate of change is important for understanding the sensitivity of tumor cells to drugs and finding appropriate therapies. It is often possible to test for differences in population means using t-test or ANOVA when the group of N samples is distinct. However, these statistical methods can not be used unless the groups are distinguished as the data covered in this paper. Statistical methods have been studied to test heterogeneity between samples. The minimum combination t-test method is one of them. In this paper, we propose a maximum combinatorial t-test method that takes into account combinations that bisect data at different ratios. Also we propose a method based on the idea that examining the heterogeneity of a sample is equivalent to testing whether the number of optimal clusters is one in the cluster analysis. We verified that the proposed methods, maximum combination t-test method and gap statistic, have better type-I error and power than the previously proposed method based on simulation study and obtained the results through real data analysis.

• Journal of the Korean Society of Marine Environment & Safety
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• v.16 no.4
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• pp.381-386
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• 2010

We have cultured the bluefin tuna in Yokjido, Tongyeong with floating cage which was vulnerable to harmful dinoflagellate, Cochiodinium polykrikoides. This study inspected a vertical migration of phytoplankton and Chl-a for reasonable sinking depth in floating cage. Furthermore, we analyzed the fluctuation of the phytoplankton including harmful dinoflagellates occurring in Yokgido for 6 years. Total cell density showed a significant monthly variation and the flora was predominated with diatoms. Gymnodinium sp. occurred 19 times, the greatest number of occurrence in all kinds of dinoflagellates during summer. In particular, the total number of occurrence at C. polykrikoides was 8, and harmful dinoflagellates such as Karenia brevis/Fibrcapsa japonica occurred. The relationship between Chl-a concentration/total cell number and sunset/sunrise was significant and reasonable sinking depth in floating cage was found to be at least 3m from the water surface, which was associated with massive fish kills caused by C. polykrikoides.

• Journal of Life Science
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• v.26 no.3
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• pp.282-288
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• 2016

Protein-protein interactions regulate the subcellular localization and function of receptors, enzymes, and cytoskeletal proteins. Proteins containing the postsynaptic density-95/disks large/zonula occludens-1 (PDZ) domain have potential to act as scaffolding proteins and play a pivotal role in various processes, such as synaptic plasticity, neural guidance, and development, as well as in the pathophysiology of many diseases. Multi-PDZ domain protein 1 (MUPP1), which has 13 PDZ domains, has a scaffolding function in the clustering of surface receptors, organization of signaling complexes, and coordination of cytoskeletal dynamics. However, the cellular function of MUPP1 has not been fully elucidated. In the present study, a yeast two-hybrid system was used to identify proteins that interacted with the N-terminal PDZ domain of MUPP1. The results revealed an interaction between MUPP1 and Wdpcp (formerly known as Fritz). Wdpcp was identified as a planar cell polarity (PCP) effector, which is known to have a role in collective cell migration and cilia formation. Wdpcp bound to the PDZ1 domain but not to other PDZ domains of MUPP1. The C-terminal end of Wdpcp was essential for the interaction with MUPP1 in the yeast two-hybrid assay. This interaction was further confirmed in a glutathione S-transferase (GST) pull-down assay. When coexpressed in HEK-293T cells, Wdpcp was coimmunoprecipitated with MUPP1. In addition, MUPP1 colocalized with Wdpcp at the same subcellular region in cells. Collectively, these results suggest that the MUPP1-Wdpcp interaction could modulate actin cytoskeleton dynamics and polarized cell migration.

• Journal of Aquaculture
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• v.10 no.4
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• pp.457-462
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• 1997

During the period of the Cochlodinium polykrikoides red tide occurrence in the southern coast of Korea in 1997, we obseved the vertical migration of red tide organisms in situ, along with environmental factors such as water temperature, dissolved oxygen, pH, chlorophyll $\alpha$ and nutrients for practical application of loess suspension techniques ot diminish fisheries damage. To cope with serious outbreaks of red tide of C. polykrikoides, the finfish culturists resorted with loess suspension to disperse the bloom watermass by turning around it with fishing boats in full speed. Peak in afternoon the cell numbers were diminished in the surface layer after sunset red tide organisms settled down in the middle and bottom layer progressively again after sunrise. Chlorophyll $\alpha$ and dissolved oxygen showed the same trends of variation with the cell number. In the course of controlling the red tide with loess suspension we could not find any severs oxygen deficiency to kill the culture species.

• Korean Journal of Ecology and Environment
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• v.53 no.1
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• pp.31-45
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• 2020

The biological indices based on the community structure with species richness and/or abundance are commonly used to assess aquatic ecosystem health. Meanwhile, recently functional traits-based approach is considered in ecosystem health assessment to reflect ecosystem functioning. In this study, we developed a database of biological traits for 136 taxa consisting of major stream insects (Ephemeroptera, Plecoptera, Trichoptera, Coleoptera, and Odonata) collected at Korean streams on the nationwide scale. In addition, we obtained environmental variables in five categories (geography, climate, land use, hydrology and physicochemistry) measured at each sampling site. We evaluated the relationships between community indices based on taxonomic diversity and functional diversity estimated from biological traits. We classified sampling sites based on similarities of their environmental variables and evaluated relations between clusters of sampling sites and diversity indices and biological traits. Our results showed that functional diversity was highly correlated with Shannon diversity index and species richness. The six clusters of sampling sites defined by a hierarchical cluster analysis reflected differences of their environmental variables. Samples in cluster 1 were mostly from high altitude areas, whereas samples in cluster 6 were from lowland areas. Non-metric multidimensional scaling (NMDS) displayed similar patterns with cluster analysis and presented variation of taxonomic diversity and functional diversity. Based on NMDS and community-weighted mean trait value matrix, species in clusters 1-3 displayed the resistance strategy in the life history strategy to the environmental variables whereas species in clusters 4-6 presented the resilience strategy. These results suggest that functional diversity can complement the biological monitoring assessment based on taxonomic diversity and can be used as biological monitoring assessment tool reflecting changes of ecosystem functioning responding to environmental changes.

• Journal of Life Science
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• v.24 no.6
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• pp.664-670
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• 2014

In the present study, we investigate the role of V. vulnificus in promoting the inflammation of mouse ileal ephitelium and its related signaling pathways. ICR mice were infected orally with V. vulnificus ($1{\times}10^9CFU$) for 16 h as a representative model of food-borne infection. To find the major portal of entry of V. vulnificus in mouse intestine, we have measured the levels of bacterial colonization in small intestine, colon, spleen, and liver. V. vulnificus appeared to colonize in intestine and colon in the order of ileum >> jejunum> colon, but lack in the duodenum, spleen, and liver. V. vulnificus in ileum caused severe necrotizing enteritis and showed shortened villi heights accompanied by an expanded width and inflammation, compared with the control mice. V. vulnificus induced ileal epithelium inflammation by activating phosphorylation of PKC and membrane translocation of $PKC{\alpha}$. V. vulnificus induced the phosphorylation of ERK and JNK, but did not affect p38 MAPK phosphorylation. Notably, V. vulnificus stimulated the I-${\kappa}B$-dependent phosphorylation of NF-${\kappa}B$ in mouse ileal epithelium. Finally, the ileal infection of V. vulnificus resulted in a significant increase in expression of proinflammatory cytokines and Toll-like receptors, respectively, compared to the control. Collectively, our results indicate that V. vulnificus induces ileal epithelium inflammation by increasing NF-${\kappa}B$ phosphorylation via activation of PKC, ERK, and JNK, which is critical for host defense mechanism in food-borne infection by V. vulnificus.