• Genomics & Informatics
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• v.7 no.3
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• pp.141-147
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• 2009

Developed proteome-scale ortholog and paralog prediction methods are mainly based on sequence similarity. However, it is known that even the closest BLAST hit often does not mean the closest neighbor. For this reason, we added conserved interaction information to find orthologs. We propose a genome-scale, automated ortholog prediction method, named OrthoInterBlast. The method is based on both sequence and interaction similarity. When we applied this method to fly and yeast, 17% of the ortholog candidates were different compared with the results of Inparanoid. By adding protein-protein interaction information, proteins that have low sequence similarity still can be selected as orthologs, which can not be easily detected by sequence homology alone.

• 한국생물공학회:학술대회논문집
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• 2005.04a
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• pp.18-18
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• 2005

Photoinduced electron transport process in nature such as photoelectric conversion and long-range electron transfer in photosynthetic organisms are known to occur not only very efficiently but also unidirectionally through the functional groups of biomolecules. The basic principles in the development of new functional devices can be inspired from the biological systems such as molecular recognition, electron transfer chain, or photosynthetic reaction center. By mimicking the organization of the biological system, molecular electronic devices can be realized $artificially^{1)}$. The nano-fabrication technology of biomolecules was applied to the development of nano-protein chip for simultaneously analyzing many kinds of proteins as a rapid tool for proteome research. The results showed that the self-assembled protein layer had an influence on the sensitivity of the fabricated bio-surface to the target molecules, which would give us a way to fabricate the nano-protein chip with high sensitivity. The results implicate that the biosurface fabrication using self-assembled protein molecules could be successfully applied to the construction of nanoscale bio-photodiode and nano-protein chip based on electrical detection.

• Asian Pacific Journal of Cancer Prevention
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• v.13 no.8
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• pp.3905-3909
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• 2012

Ovarian cancer is the fifth leading cause of cancer death in women aged 35 to 74 years. Although there are several popular hypothesis of ovarian cancer pathogenesis, the genetic mechanisms are far from being clear. Recently, systems biology approaches such as network-based methods have been successfully applied to elucidate the mechanisms of diseases. In this study, we constructed a crosstalk network among ovarian cancer related pathways by integrating protein-protein interactions and KEGG pathway information. Several significant pathways were identified to crosstalk with each other in ovarian cancer, such as the chemokine, Notch, Wnt and NOD-like receptor signaling pathways. Results from these studies will provide the groundwork for a combination therapy approach targeting multiple pathways which will likely be more effective than targeting one pathway alone.

• Journal of the Korean Wood Science and Technology
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• v.39 no.1
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• pp.21-27
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• 2011

This study was carried out to examine properties of water resistant plywood by using serum protein adhesive which is natural, environment-friendly and human-friendly. For the preparation of the serum protein adhesive, pig blood from slaughterhouse was centrifuged and serum was separated from corpuscles and concentrated to 30% by dry weight basis. This concentrated serum protein was modified with PF resin (50% NVC) with the ratio of 9 : 2.5. Plywood made by this modified serum protein gave 1.21 N/$mm^2$ of dry bonding strength, 0.80 N/$mm^2$ of wet boil bonding strength, 0% of cyclic delamination test value, and 0.025 ppm of HCHO emission, which met the excellent super $E_0$ grade and water resistant plywood.

• Genomics & Informatics
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• v.21 no.2
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• pp.25.1-25.12
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• 2023

Adaptation of infections and hosts has resulted in several metabolic mechanisms adopted by intracellular pathogens to combat the defense responses and the lack of fuel during infection. Human tuberculosis caused by Mycobacterium tuberculosis (MTB) is the world's first cause of mortality tied to a single disease. This study aims to characterize and anticipate potential antigen characteristics for promising vaccine candidates for the hypothetical protein of MTB through computational strategies. The protein is associated with the catalyzation of dithiol oxidation and/or disulfide reduction because of the protein's anticipated disulfide oxidoreductase properties. This investigation analyzed the protein's physicochemical characteristics, protein-protein interactions, subcellular locations, anticipated active sites, secondary and tertiary structures, allergenicity, antigenicity, and toxicity properties. The protein has significant active amino acid residues with no allergenicity, elevated antigenicity, and no toxicity.

• Advanced Composite Materials
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• v.16 no.4
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• pp.269-282
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• 2007

Fully biodegradable high strength composites or 'advanced green composites' were fabricated using yearly renewable soy protein based resins and high strength liquid crystalline cellulose fibers. For comparison, E-glass and aramid ($Kevlar^{(R)}$) fiber reinforced composites were also prepared using the same modified soy protein resins. The modification of soy protein included forming an interpenetrating network-like (IPN-like) resin with mechanical properties comparable to commonly used epoxy resins. The IPN-like soy protein based resin was further reinforced using nano-clay and microfibrillated cellulose. Fiber/resin interfacial shear strength was characterized using microbond method. Tensile and flexural properties of the composites were characterized as per ASTM standards. A comparison of the tensile and flexural properties of the high strength composites made using the three fibers is presented. The results suggest that these green composites have excellent mechanical properties and can be considered for use in primary structural applications. Although significant additional research is needed in this area, it is clear that advanced green composites will some day replace today's advanced composites made using petroleum based fibers and resins. At the end of their life, the fully sustainable 'advanced green composites' can be easily disposed of or composted without harming the environment, in fact, helping it.

• Asian-Australasian Journal of Animal Sciences
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• v.21 no.11
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• pp.1624-1628
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• 2008

Experiments were conducted to evaluate the nutritional value of yellow-seeded rapeseed meal (YRSM). In the first experiment nutrient retention was recorded by 48 Arbor Acres-broiler chickens (28-d old) to determine AMEn (nitrogen-corrected apparent metabolizable energy), coefficient of apparent protein digestibility based on ileal digesta nitrogen, excreta nitrogen and uric acid nitrogen. The second experiment was carried out with 304 Arbor Acres-broiler chickens to compare effects of SBM (soybean meal) and YRSM on performance, carcass and digestive tract status. In the control treatment, SBM was replaced by graded levels of YRSM at 15, 22.5 and 30% of diet. Digestibility of YRSM protein was significantly lower (p<0.001) than SBM protein. The protein digestibility based on ileal measurement was significantly higher (p<0.001) than protein digestibility from excreta samples. There was no significant difference (p>0.001) between ileal and excreta digestibility of protein based on uric acid. AMEn as a fraction of gross energy was 0.54 in SBM and 0.45 in YRSM. With the exception of 30% YRSM, other YRSM treatments resulted in major effects on length and weight of the gastrointestinal tract. The results of this study have shown no adverse effect on performance as well as protein digestibility and energy value in response to replacement of SBM by YRSM with the exception of 22.5 and 30% YRSM.

• The Plant Pathology Journal
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• v.26 no.1
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• pp.25-31
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• 2010

Papaya ringspot virus (PRSV) causes the most widespread and devastating disease in papaya. Isolates of PRSV originating from different geographical regions in south India were collected and maintained on natural host papaya. The entire coat protein (CP) gene of Papaya ringspot virus-P biotype (PRSV-P) was amplified by RTPCR. The amplicon was inserted into pGEM-T vector, sequenced and sub cloned into a bacterial expression vector pRSET-A using a directional cloning strategy. The PRSV coat protein was over-expressed as a fusion protein in Escherichia coli. SDS-PAGE gel revealed that CP expressed as a ~40 kDa protein. The recombinant coat protein (rCP) fused with 6x His-tag was purified from E.coli using Ni-NTA resin. The antigenicity of the fusion protein was determined by western blot analysis using antibodies raised against purified PRSV. The purified rCP was used as an antigen to produce high titer PRSV specific polyclonal antiserum. The resulting antiserum was used to develop an immunocapture reverse transcription-polymerase chain reaction (IC-RT-PCR) assay and compared its sensitivity levels with ELISA based assays for detection of PRSV isolates. IC-RT-PCR was shown to be the most sensitive test followed by dot-blot immunobinding assay (DBIA) and plate trapped ELISA.

• Journal of the Korean Magnetic Resonance Society
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• v.19 no.3
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• pp.112-118
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• 2015

Hsp31 protein is one of the members of DJ-1 superfamily proteins and has a dimeric structure of which molecular weight (MW) is 62 kDa. The mutation of DJ-1 is closely related to early onset of Parkinson's disease. Hsp31 displays $Zn^{+2}$-binding activity and was first reported to be a holding chaperone in E. coli. Its additional glyoxalase III active has recently been characterized. Moreover, an incubation at $60^{\circ}C$ induces Hsp31 protein to form a high MW oligomer (HMW) in vitro, which accomplishes an elevated holding chaperone activity. The NMR technique is elegant method to probe any local or global structural change of a protein in responses to environmental stresses (heat, pH, and metal). Although the presence of the backbone chemical shifts (bbCSs) is a prerequisite for detailed NMR analyses of the structural changes, general HSQC-based triple resonance experiments could not be used for 62 kDa Hsp31 protein. Here, we prepared the per-deuterated Hsp31 and performed the TROSY-based triple resonance experiments for the bbCSs assignment. Here, detailed processes of per-deuteration and the NMR experiments are described for other similar NMR approaches.

• Journal of the Korea Society of Computer and Information
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• v.14 no.3
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• pp.193-207
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• 2009

Intracellular signal transduction is achieved by protein-protein interaction. In this paper, we suggest high performance algorithm based on Yeast protein-protein interaction and protein location information. We compare if pathways predicted with high valued weights indicate similar tendency with pathways provided in KEGG. Furthermore, we suggest extracted results, which can imply a discovery of new signaling pathways that is yet proven through experiments. This will be a good basis for research to discover new protein signaling pathways and unknown functions of established proteins.