• BMB Reports
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• v.37 no.1
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• pp.83-92
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• 2004

As a result of the enormous amount of information that has been collected with E. coli over the past half century (e.g. genome sequence, mutant phenotypes, metabolic and regulatory networks, etc.), we now have detailed knowledge about gene regulation, protein activity, several hundred enzyme reactions, metabolic pathways, macromolecular machines, and regulatory interactions for this model organism. However, understanding how all these processes interact to form a living cell will require further characterization, quantification, data integration, and mathematical modeling, systems biology. No organism can rival E. coli with respect to the amount of available basic information and experimental tractability for the technologies needed for this undertaking. A focused, systematic effort to understand the E. coli cell will accelerate the development of new post-genomic technologies, including both experimental and computational tools. It will also lead to new technologies that will be applicable to other organisms, from microbes to plants, animals, and humans. E. coli is not only the best studied free-living model organism, but is also an extensively used microbe for industrial applications, especially for the production of small molecules of interest. It is an excellent representative of Gram-negative commensal bacteria. E. coli may represent a perfect model organism for systems biology that is aimed at elucidating both its free-living and commensal life-styles, which should open the door to whole-cell modeling and simulation.

• Journal of the Korean Society of Environmental Restoration Technology
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• v.9 no.6
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• pp.162-167
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• 2006

The urban stream includes the channel and sandbars. The sandbar plays a key role in the riparian ecosystem. For birds and insects the sandbar offers a small strip of habitat and fish and other fauna feed in the boundary of sandbar where eddies occur. So, it is important habitat and source for the flow of energy, matter and organisms through the landscape and act as ecotone between the terrestrial and stream corridors. However, the sandbar changes continuously by the natural process. Thus, it is necessary to measure the shape and area of the sandbar accurately for the efficient urban stream management for the amenity of urban residents and stream protection. The study site is Yangjae Stream where the first natural-style urban stream restoration projected was impelemented by the support of Ministry of Education in Korea. The measurement was taken by the beacon Differential Global Positioning System (DGPS) and the data were stored and analyzed using ArcView Geographic Information System (GIS) program. Therefore, the purpose of this study is to measure the change of sandbars in the urban stream after concentrated stormwater during summer.

• Korean Journal of Fisheries and Aquatic Sciences
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• v.46 no.1
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• pp.59-69
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• 2013

Temporal and spatial variation in the freshwater region, created by river runoff, of a small bay, caused by the passage of typhoons was examined using a three-dimensional primitive equation model (the Princeton Ocean Model, POM). Numerical experiments were implemented focusing on temporal evolution in the freshwater region in association with typhoon tracks. The model domain covered most of the estuary around the Nakdong River, including Noksan Bay, where river water is periodically released from upstream (Noksan dam). The model showed that the extension of the freshwater region outside of the bay depended strongly on the tracks of typhoons, specifically the associated wind directions and inner flow fields that are accompanied by new clockwise eddies. The model also showed that entrainment from typhoon passage frequently creates salt wedges in the estuary, indicating that organisms in the bay are biologically and chemically influenced with variation in the freshwater region.

• Journal of Fisheries and Marine Sciences Education
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• v.27 no.1
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• pp.49-62
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• 2015

As methods reducing damages by jellyfish which enter the coastal areas of Korea, attaching cutting devices to towing nets of otter trawls or pair trawls and/or using a canvas type of cutting nets of small fishing boats have been widely utilized. In order to reduce shut-down damages of power plants in coastal areas due to the mass influx of marine organisms including jellyfish, a possible improvement of the traveling water screen system and various jellyfish influx blocking devices were suggested in this study. The results could be utilized as an important index for reducing damages by jellyfish bloom which cause on a massive scale in summer in Korea.

• Journal of Wetlands Research
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• v.18 no.1
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• pp.1-9
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• 2016

Areas around of National Park have been severed eco-corridor of wildlife due to urban expansion and development. Habitats have been fragmented into small pieces. Habitat fragmentation reduces the biodiversity of organisms because the exchange loss and inbreeding of wild fauna and flora. The main cause of the fragmentation of ecological networks in areas around of Moodeungsan National Park are are that the cemetery, cutting of mountain, roads, public parking lots, mountain encroachment by land, urban infrastructure, electric transmission towers, urban area. Area around of National Park must be equipped with ecological networks through an ecological design that can communicate with each other in the national park and urban areas.

• Journal of Microbiology
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• v.39 no.3
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• pp.149-153
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• 2001

The electron transfer reaction is one of the most essential processes of life. Not only does it provide the means of transforming solar and chemical energy into a utilizable form for all living organisms, it also extends into a range of metabolic processes that support the life of a cell. Thus, it is of great interest to understand the physical basis of the rates and reduction potentials of these reactions. To identify the major determinants of reduction potentials in redox proteins, we have chosen the simplest electron transfer protein, rubredoxin, a small (52-54 residue) iron-sulfur protein family, widely distributed in bacteria and archaea. Rubredoxins can be grouped into two classes based on the correlation of their reduction potentials with the identity of residue 44; those with Ala44 (ex: Pyrococcus furiosus) have reduction potentials that are ∼50 mV higher than those with Va144 (ex: Clostridium pasteurianum). Based on the crystal structures of rubredoxins from C. pasteurianum and P. furiosus, we propose the identity of residue 44 alone determines the reduction potential by the orientation of the electric dipole moment of the peptide bond between 43 and 44. Based on 1.5 $\AA$ resolution crystal structures and molecular dynamics simulations of oxidized and reduced rubredoxins from C. pasteurianum, the structural rearrangements upon reduction suggest specific mechanisms by which electron transfer reactions of rubredoxin should be facilitated.

• Journal of Environmental Health Sciences
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• v.38 no.4
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• pp.351-359
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• 2012

Objectives: This study was conducted in order to investigate the specific correlation between physicochemical properties and bioactivity in ecdysteroids found in living organisms. Methods: The examined steroidal compounds were classified into three groups according to their relevance to ecdysone activity. Each compound molecule was completely drawn to automatically calculate its physicochemical parameters and docked against 20-hydroxyecdysone to calculate the total distance. Electronic charge distribution was also observed for each molecule. All procedures were conducted using a computational chemistry program. Results: Ecdysone agonists showed different ranges of parameter values, such as log P, hydrophilic-lipophilic balance (HLB), solubility parameter (SP), hydrophilic surface (HPS), hydrogen bond (HB) and Kappa 2, when compared with antagonists and steroids without ecdysone activity. They also showed a similar electronic charge distribution that is significantly different from the electron charge distribution of antagonists and steroids without ecdysone activity. The total distance values of agonists, estimated by docking them with 20-hydroxyecdysone, were relatively small but showed no correlation with binding affinity with receptor ligand. Conclusions: These results suggest that physicochemical properties such as steric and electronic effects, hydrophobicity and hydrogen bonding may operate in combination to determine the binding activity of ecdysteroids to the receptor protein.

• Molecules and Cells
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• v.40 no.11
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• pp.805-813
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• 2017

The role of phospholipase D (PLD) in cancer development and management has been a major area of interest for researchers. The purpose of this mini-review is to explore PLD and its distinct role during chemotherapy including anti-apoptotic function. PLD is an enzyme that belongs to the phospholipase super family and is found in a broad range of organisms such as viruses, yeast, bacteria, animals, and plants. The function and activity of PLD are widely dependent on and regulated by neurotransmitters, hormones, small monomeric GTPases, and lipids. A growing body of research has shown that PLD activity is significantly increased in cancer tissues and cells, indicating that it plays a critical role in signal transduction, cell proliferation, and anti-apoptotic processes. In addition, recent studies show that PLD is a downstream transcriptional target of proteins that contribute to inflammation and carcinogenesis such as Sp1, $NF{\kappa}B$, TCF4, ATF-2, NFATc2, and EWS-Fli. Thus, compounds that inhibit expression or activity of PLD in cells can be potentially useful in reducing inflammation and sensitizing resistant cancers during chemotherapy.

• ALGAE
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• v.31 no.4
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• pp.289-301
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• 2016

Floating debris provides substrates for dispersal of organisms by ocean currents, including algae that thrive on plastics. The 2011 earthquake and tsunami in Tohuku, Japan resulted in large amounts of debris carried by the North Pacific Current to North America from 2012 to 2016. In 2015-2016, the plastics in the debris bore a complex biota including pink algal crusts. One sample (JAW4874) was isolated into culture and a three-gene phylogeny (psbA, rbcL, and SSU) indicated it was an unknown member of the red algal class Stylonematophyceae. It is a small pulvinate crust of radiating, branched, uniseriate filaments with cells containing a single centrally suspended nucleus and a single purple to pink, multi-lobed, parietal plastid lacking a pyrenoid. Cells can be released as spores that attach and germinate to form straight filaments by transverse apical cell divisions, and subsequent longitudinal and oblique intercalary divisions produce masses of lateral branches. This alga is named Tsunamia transpacifica gen. nov. et sp. nov. Sequencing of additional samples of red algal crusts on plastics revealed another undescribed Stylonematophycean species, suggesting that these algae may be frequent on drift oceanic plastics.

• The Plant Pathology Journal
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• v.25 no.2
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• pp.184-188
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• 2009

Identification of differently expressed genes under specific tissues and/or environments provides insights into the nature and underlying mechanisms of cellular processes. Although cDNA-AFLP (Amplified Fragment Length Polymorphism) is a powerful method for analyzing differentially expressed genes, its use has been limited to the requirement of radioactive isotope use and the difficulty of isolating the bands of interest from a gel. Here, we describe a modified method for cDNA-AFLP that uses a fluorescence dye for detection and isolation of bands directly from a small size polyacrylamide gel. This method involves three steps: (i) preparation of cDNA templates, (ii) PCR amplification and differential display, and (iii) identification of differentially expressed genes. To demonstrate its utility and efficiency, differentially expressed genes during vegetative growth and appressorial development of Magnaporthe oryzae were analyzed. This method could be applied to compare gene expression profiles in a diverse array of organisms.