• Advances in nano research
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• v.1 no.3
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• pp.133-151
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• 2013

The availability of advanced nanotechnological methodologies (experimental and theoretical) has widened the investigation of biological/organic matter in interaction with substrates. Minerals are good candidates as substrates because they may present a wide variety of physico-chemical properties and surface nanostructures that can be used to actively condense and manipulate the biomolecules. Scanning Probe Microscopy (SPM) is one of the best suited techniques used to investigate at a single molecule level the surface interactions. In addition, the recent availability of high performance computing has increased the possibility to study quantum mechanically the interaction phenomena extending the number of atoms involved in the simulation. In the present paper, firstly we will briefly introduce new SPM technological developments and applications to investigate mineral surfaces and mineral-biomolecule interaction, then we will present results on the specific RNA-mineral interaction and recent basics and applicative achievements in the field of the interactions between other fundamental biological molecules and mineral surfaces from both an experimental and theoretical point of view.

• Genomics & Informatics
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• v.1 no.1
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• pp.1-6
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• 2003

In conclusion, the seemingly fuzzy and disorganized data of biology with thousands of different layers ranging from molecule to the Internet have refused so far to be mapped precisely and predicted successfully by mathematicians, physicists or computer scientists. Genomics and bioinformatics are the fields that process such complex data. The insights on the nature of biological entities as complex interaction networks are opening a door toward a generalization of the representation of biological entities. The main challenge of genomics and bioinformatics now lies in 1) how to data mine the networks of the domains of bioinformatics, namely, the literature, metabolic pathways, and proteome and structures, in terms of interaction; and 2) how to generalize the networks in order to integrate the information into computable genomic data for computers regardless of the levels of layer. Once bioinformatists succeed to find a general principle on the way components interact each other to form any organic interaction network at genomic scale, true simulation and prediction of life in silico will be possible.

• Genomics & Informatics
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• v.2 no.2
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• pp.99-106
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• 2004

In this paper we introduce PubMiner, an intelligent machine learning based text mining system for mining biological information from the literature. PubMiner employs natural language processing techniques and machine learning based data mining techniques for mining useful biological information such as protein­protein interaction from the massive literature. The system recognizes biological terms such as gene, protein, and enzymes and extracts their interactions described in the document through natural language processing. The extracted interactions are further analyzed with a set of features of each entity that were collected from the related public databases to infer more interactions from the original interactions. An inferred interaction from the interaction analysis and native interaction are provided to the user with the link of literature sources. The performance of entity and interaction extraction was tested with selected MEDLINE abstracts. The evaluation of inference proceeded using the protein interaction data of S. cerevisiae (bakers yeast) from MIPS and SGD.

• Journal of Applied Biological Chemistry
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• v.57 no.1
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• pp.33-40
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• 2014

Polysaccharides have attracted great attention for their wide range of applications in biological and medical fields. In this paper, the interaction of polysaccharides with human serum albumin (HSA) was systematically investigated by fluorescence (FL) spectroscopy and circular dichroism (CD) spectra under different conditions. The Stern-Volmer quenching constants ($K_a$) at different ionic strength and pH were calculated, and information of the structural features of HSA was discussed. FL and CD results indicate that both hydrophobic and electrostatic interactions play important roles during the binding process. The quenching of the fluorescence resulting the binding of polysaccharides and HSA is static.

• Genomics & Informatics
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• v.1 no.1
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• pp.7-19
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• 2003

The latest measure of the relative evolutionary age of protein structure families was applied (based on taxonomic diversity) using the protein structural interactome map (PSIMAP). It confirms that, in general, protein domains, which are hubs in this interaction network, are older than protein domains with fewer interaction partners. We apply a hypothesis of 'biological network evolution' to explain the positive correlation between interaction and age. It agrees to the previous suggestions that proteins have acquired an increasing number of interaction partners over time via the stepwise addition of new interactions. This hypothesis is shown to be consistent with the scale-free interaction network topologies proposed by other groups. Closely co-evolved structural interaction and the dynamics of network evolution are used to explain the highly conserved core of protein interaction pathways, which exist across all divisions of life.

• Korea-Australia Rheology Journal
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• v.16 no.3
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• pp.135-140
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• 2004

Morphological and rheological properties of the poly(methyl methacrylate) (PMMA) and polystyrene (PS) blends were studied by scanning electron microscopy (SEM) and advanced rheometric expansion system (ARES). From the SEM results, the PMMA-PS blends showed dispersed morphology and the particle size of the dispersed phase was quite small (0.1~0.6 $\mu\textrm{m}$ compared with other immiscible polymer blends. Values of the interfacial tension of the PMMA-PS blend were obtained from the Choi-Schowalter and the Palierne emulsion models using the storage modulus of the PMMA and PS, and found to be 1.0 and 2.0 mN/m, respectively. The interfacial tension between the PMMA and PS was also calculated from the Flory-Huggins polymer-polymer interaction parameter ($\chi$) and found to be from 0.98 to 1.86 mN/m depending on the molecular weight and composition. Comparing the values of the interfacial tension from the Flory-Huggins polymer-polymer interaction parameter and the values measured by oscillatory rheometer, it is suggested that the interfacial tension of the PMMA-PS blend obtained from the polymer-polymer interaction parameter are in good agreement with the values obtained by rheological measurements.

• Animal cells and systems
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• v.6 no.3
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• pp.277-282
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• 2002

Topoisomearse II is an essential enzyme in all organisms with several independent roles in DNA metabolism. Recently, it has been demonstrated that the C-terminal region of topoisomerases II is associated with hetero-logous protein-protein interactions in human and yeast. In this study, we identified that RTP1, a rat homologue of EIA binding protein BS69, is another topoisomerae II interacting protein by yeast two-hybrid screening. RTP1 has an E1A-binding domain and a MYND motif, which are known to be required for transcriptional regulation by binding to other proteins and interaction with the leucine zipper motif of topoisomerase II. The physical interaction between RTP1 and topoisomerase ll$\alpha$ was examined by GST pull-down assay in vitro. The expression level of RTP1 peaks in S phase as that of topoisomerase ll$\alpha$. These results suggest that the interaction between topoisomerase ll$\alpha$ and RTP1 might play an important role in regulating the transcription of genes involved in DNA metabolism in higher eukaryotes.

• Korean Journal of Ecology and Environment
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• v.56 no.1
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• pp.104-125
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• 2023

The predator-prey interaction in freshwater ecosystems is a crucial area in the ecological study field and one of example to find such interaction is to investigate stomach contents. However, traditional method through visual inspection often induce misidentification, as it depends critically on intactness of physically visible data. In this study, we utilized Next-Generations Sequencing (NGS) technology to test the applicability stomach content analysis and overcome such limitation. NGS was applied to analyze the stomach contents of the Hemibarbus labeo, Tachysurus fulvidraco, and Plecoglossus altivelis collected in the lower part of Nakdong River. As a result, T. fulvidraco had a higher number of Animalia operational taxonomic units (OTUs) intake rate than H. labeo. At the same time, P. altivelis had higher number of Plantae OTUs intake rate than T. fulvidraco and higher Protozoa OTUs intake rate than H. labeo respectively. Therefore, NGS technology application enable to overcome traditional method's limitation and discover hidden interspecific interaction which can further be used in appropriate habitat assessment.

• Korea-Australia Rheology Journal
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• v.14 no.4
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• pp.203-207
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• 2002

Particle-particle interaction is of great importance in the study of suspension rheology. In this research we have investigated the hydrodynamic interaction between two identical cylinders in viscoelastic fluids numerically as a model problem for the study of viscoelastic suspension. We confine two neutrally buoyant cylinders between two parallel plates and impose a shear flow. We determine the migration velocity of two cylinders. The result shows that cylinders move toward or away from each other depending upon the initial distance between them and that there is an equilibrium distance between two cylinders in viscoelastic fluids regardless of the initial distance. In the case of Newtonian fluid, there is no relative movement as expected. The results partly explain the chaining phenomena of spherical particles in shear flows of viscoelastic fluids.

• Journal of Microbiology and Biotechnology
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• v.18 no.3
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• pp.472-476
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• 2008

Two isoforms of human CD99 have been identified, but only heterotypic interaction between the isomers was recently demonstrated. In this study, we performed bimolecular fluorescence complementation analysis to further characterize the interaction in vivo. Upon transiently transfecting plasmids expressing either of the two isoforms fused with yellow fluorescent protein (YFP) fragments, all the YFP-tagged CD99 molecules were properly localized on cell surfaces, and formed fluorescent dimers. Interestingly, however, unlike the previous report, the homodimers formed as efficiently as the heterodimer via their extracellular domains, implying its distinct regulatory role through modulating the complex profile.