• Korean Journal of Ecology and Environment
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• v.53 no.4
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• pp.336-343
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• 2020

Large-scale cultivation of Microcystis aeruginosa in different light conditions was conducted for verifying the cell growth in a greenhouse system. Environmental and chemical parameters of the large-scale culture medium were measured for analyzing the interaction between M. aeruginosa and its symbiotic bacteria. During cultivation, a difference in cell growth pattern was observed between control (natural light) and light-limited groups (reduction of blue, green, and blue/green light, respectively). Comparing the control group, the light reduced groups showed slow and delayed cell growth through the cultivation period. Also, there is differences in the consuming pattern of total nitrogen and total phosphorus which indicated that the possibility of interaction between M. aeruginosa and symbiotic bacteria.

• Proceedings of the Korean Vacuum Society Conference
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• 2005.08a
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• pp.57-57
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• 2005

• Molecules and Cells
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• v.41 no.9
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• pp.842-852
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• 2018

Notch signaling is an evolutionarily conserved pathway and involves in the regulation of various cellular and developmental processes. Ligand binding releases the intracellular domain of Notch receptor (NICD), which interacts with DNA-bound CSL [CBF1/Su(H)/Lag-1] to activate transcription of target genes. In the absence of NICD binding, CSL down-regulates target gene expression through the recruitment of various corepressor proteins including SMRT/NCoR (silencing mediator of retinoid and thyroid receptors/nuclear receptor corepressor), SHARP (SMRT/HDAC1-associated repressor protein), and KyoT2. Structural and functional studies revealed the molecular basis of these interactions, in which NICD coactivator and corepressor proteins competitively bind to ${\beta}-trefoil$ domain (BTD) of CSL using a conserved ${\varphi}W{\varphi}P$ motif (${\varphi}$ denotes any hydrophobic residues). To date, there are conflicting ideas regarding the molecular mechanism of SMRT-mediated repression of CSL as to whether CSL-SMRT interaction is direct or indirect (via the bridge factor SHARP). To solve this issue, we mapped the CSL-binding region of SMRT and employed a 'one- plus two-hybrid system' to obtain CSL interaction-defective mutants for this region. We identified the CSL-interaction module of SMRT (CIMS; amino acid 1816-1846) as the molecular determinant of its direct interaction with CSL. Notably, CIMS contains a canonical ${\varphi}W{\varphi}P$ sequence (APIWRP, amino acids 1832-1837) and directly interacts with CSL-BTD in a mode similar to other BTD-binding corepressors. Finally, we showed that CSL-interaction motif, rather than SHARP-interaction motif, of SMRT is involved in transcriptional repression of NICD in a cell-based assay. These results strongly suggest that SMRT participates in CSL-mediated repression via direct binding to CSL.

• Genomics & Informatics
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• v.10 no.4
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• pp.256-262
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• 2012

Most common complex traits, such as obesity, hypertension, diabetes, and cancers, are known to be associated with multiple genes, environmental factors, and their epistasis. Recently, the development of advanced genotyping technologies has allowed us to perform genome-wide association studies (GWASs). For detecting the effects of multiple genes on complex traits, many approaches have been proposed for GWASs. Multifactor dimensionality reduction (MDR) is one of the powerful and efficient methods for detecting high-order gene-gene ($G{\times}G$) interactions. However, the biological interpretation of $G{\times}G$ interactions identified by MDR analysis is not easy. In order to aid the interpretation of MDR results, we propose a network graph analysis to elucidate the meaning of identified $G{\times}G$ interactions. The proposed network graph analysis consists of three steps. The first step is for performing $G{\times}G$ interaction analysis using MDR analysis. The second step is to draw the network graph using the MDR result. The third step is to provide biological evidence of the identified $G{\times}G$ interaction using external biological databases. The proposed method was applied to Korean Association Resource (KARE) data, containing 8838 individuals with 327,632 single-nucleotide polymorphisms, in order to perform $G{\times}G$ interaction analysis of body mass index (BMI). Our network graph analysis successfully showed that many identified $G{\times}G$ interactions have known biological evidence related to BMI. We expect that our network graph analysis will be helpful to interpret the biological meaning of $G{\times}G$ interactions.

• The Korean Journal of Pesticide Science
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• v.2 no.3
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• pp.1-20
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• 1998

Chlorsulfuron, one of sulfonylurea herbicides acts through inhibition of acetolactate syuthase (EC 4.1.3.18; ALS, also known as acetohydroxyacid synthase) in the branched-chain amino acid biosynthesis process. After chlorsulfuron-ALS interaction, many physiological and metabolic disruptions occur in plants. However, it is not clear how this chlorsulfuron-ALS interaction affects those physiological and metabolic processes and how this interaction leads subsequently to plant death. Several researchers suggested that the death of chlorsulfuron-treated plants might be due to a shortage of the branched-chain amino acids, an accumulation of toxic metabolites, and/or a depletion of photoassimilates. It remains as a mystery presently, however, if such changes result in the plant death. In this review, we discussed how the chlorsulfuran-ALS interaction leads to physiological and metabolic disruptions in plants.

• Journal of the Korean Society of Food Science and Nutrition
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• v.23 no.5
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• pp.867-878
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• 1994

A general overview of the lipid peroxidation and its nutritional significance are presented ,with emphasis on the reaction mechaisms, peroxidized products, further interaction and nutritional/biological deterioration in a series of oxidative process. Overall mechanism with various factors and elements for initiation , propagation and termination of free radical reaction is reviewed and the primary /secondary products of peroxidized lipids are defined. Since these products are potentially reactive substances that can cause deterioration of proteins /amino acids and vitamins (carotene, tocopherols and ascorbic acid etc), mechanism and actual damages of their deterioration in some foods and biological models are outlined. Especially , chemical changes caused by interaction of peroxidized products (related hydroperoxides, radicals and malonaldehye etc) and protein are emphasized here. And also, the detailed mechanisms on radical scavenging of the these vitamins which are the most prominent natural antioxidants are presented . Additionally , the possible roles of peroxidicaed lipids and their secondary products in the process of aging an carcinogenesis are briefly discussed . However, it is important to not that more detailed and integrated studies on the reaction kinetics, energetics of peroxidation, their decomposed products , biochemical interaction potential damaging/aging / carcinogenic effects, protection from their oxidative spoilage and novel antioxidants in food and heterogeneous biological systems will be essential in order to assessing the implication of lipid peroxidation to human nutrition and health.

• Korea-Australia Rheology Journal
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• v.19 no.3
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• pp.147-156
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• 2007

The orientation and deformation of polymer chains in a confined channel flow has been investigated. The polymer chain was modeled as a Finitely Extensible Nonlinear Elastic (FENE) dumbbell. The Brownian configuration field method was extended to take the interaction between the flow and local chain dynamics into account. Drag and Brownian forces were treated as anisotropic in order to reflect the influence of the wall in the confined flow. Both Poiseuille flow and 4 : 1 contraction flow were considered. Of particular interest was molecular tumbling of polymer chains near the wall. It was strongly influenced by anisotropic drag and high shear close to the wall. We discussed the mechanism of this particular behavior in terms of the governing forces. The dumbbell configuration was determined not only by the wall interaction but also by the flow type of the geometric origin. The effect of extensional flow on dumbbell configuration was also discussed by comparing with the Poiseuille flow.

• BMB Reports
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• v.37 no.1
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• pp.45-52
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• 2004

The goal of interaction proteomics that studies the protein-protein interactions of all expressed proteins is to understand biological processes that are strictly regulated by these interactions. The availability of entire genome sequences of many organisms and high-throughput analysis tools has led scientists to study the entire proteome (Pandey and Mann, 2000). There are various high-throughput methods for detecting protein interactions such as yeast two-hybrid approach and mass spectrometry to produce vast amounts of data that can be utilized to decipher protein functions in complicated biological networks. In this review, we discuss recent developments in analytical methods for large-scale protein interactions and the future direction of interaction proteomics.

• BMB Reports
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• v.34 no.5
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• pp.452-456
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• 2001

Surface plasmon resonance has been used for a biospecific interaction analysis between two macromolecules in real time. Determination of an antibody that is capable of specifically interacting with the native form of antigen is very useful for many biological and medical applications. Twenty monoclonal antibodies against the $\alpha$ subunit of E. coli DNA polymerase III were screened for specifically recognizing the native form of protein using surface plasmon resonance. Only four monoclonal antibodies among them specifically recognized the native $\alpha$ protein, although all of the antibodies were able to specifically interact with the denatured $\alpha$ subunit. These antibodies failed to interfere with the interaction between the $\tau$ and $\alpha$ subunits that were required for dimerization of the two polymerases at the DNA replication fork. This real-time analysis using surface plasmon resonance provides an easy method to screen antibodies that are capable of binding to the native form of the antigen molecule and determine the biological interaction between the two molecules.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2004.11a
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• pp.265-271
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• 2004

The interaction network of protein -protein plays an important role to understand the various biological functions of cells. Currently, the high -throughput experimental techniques (two -dimensional gel electrophoresis, mass spectroscopy, yeast two -hybrid assay) provide us with the vast amount of data for protein-protein interaction at the proteome scale. In order to recognize the role of each protein in their network, the efficient bioinformatical and computational analysis methods are required. We propose a systematic and mathematical method which can analyze the protein -protein interaction network rigorously and enable us to capture the biological and physical essence of a topological character and stability of protein -protein network, and sensitivity of each protein along the biological pathway of their network. We set up a Laplacian matrix of spectral graph theory based on the protein-protein network of yeast proteome, and perform an eigenvalue analysis and apply a perturbation method on a Laplacian matrix, which result in recognizing the center of protein cluster, the identity of hub proteins around it and their relative sensitivities. Identifying the topology of protein -protein network via a Laplacian matrix, we can recognize the important relation between the biological pathway of yeast proteome and the formalism of master equation. The results of our systematic and mathematical analysis agree well with the experimental findings of yeast proteome. The biological function and meaning of each protein cluster can be explained easily. Our rigorous analysis method is robust for understanding various kinds of networks whether they are biological, social, economical...etc