• Plant Biotechnology Reports
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• v.5 no.4
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• pp.309-315
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• 2011

Rice grown in anaerobic waterlogged soil accumulates ammonium as a major source of nitrogen (N). We have compared the physiological symptoms of rice seedlings subjected to N-starvation stress with those receiving sufficient N, based on measurements of shoot/root length and weight and an analysis of protein expression patterns. N starvation marginally increased root growth but notably decreased shoot biomass. N uptake was reduced by >50% in the roots and shoots of N-starved seedlings. To better understand the mechanism of N starvation in rice, we performed a comparative proteome analysis of proteins isolated from rice leaves. Twenty-five differentially expressed proteins were analyzed by matrixassisted laser desorption/ionization time-of-flight (TOF) mass spectrometry and electron spray ionization quadrupole TOF. Functional analysis of the N-starvation response proteins suggested their involvement in protein synthesis and fate, metabolism, and defense. These results indicate that these proteins may play important roles in regulating the plant's complex adaptation responses for N use during N starvation. The proteins may be useful for further characterization of protein function in plant N nutrition.

• IMMUNE NETWORK
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• v.5 no.2
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• pp.105-109
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• 2005

Background: Dendritic cells (DCs) are the most potent APCs (antigen-presenting cells) and playa critical role in immune responses. Galectin-3 is a biological lectin with a beta-galactoside binding affinity. Recently, proteomic analysis revealed the presence of galectin-3 in the exosome of mature DCs. However, the expression and function of galectin-3 in DCs remains unclear yet. Methods: We used bone marrow-derived DCs of mouse and showed the expression of galectin-3 in DCs by using flow cytometry analysis and Western blot analysis. Results: Galectin-3 was determined as single band of 35 kDa in Western blot analysis. Flow cytometry analysis showed the major growth factor for DCs, granulocyte-macrophage colony stimulating factor (GM-CSF) and maturing agents, anti-CD40 monoclonal antibody (mAb) and lipopolysaccharide (LPS) consistently increased the intracellular expression of galectin-3 in DCs compared to medium alone. In addition, DCs treated with maturing agents did marginally express galectin-3 on their surface. Conclusion: This study suggests that galectin-3 in DCs may be regulated by critical factors for DC function.

• 한국생물공학회:학술대회논문집
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• 2005.10a
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• pp.519-519
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• 2005

• Journal of The Korean Society of Integrative Medicine
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• v.10 no.2
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• pp.37-47
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• 2022

Purpose : We aimed to investigate the effects of nutritional foods on sarcopenia prevention and physical function among the elderly living in rural communities during the COVID-19 pandemic by providing customized nutrition. Methods : This study was conducted in the rural community of SCC. Participants (n=24, over age 65) were randomly assigned into a Protein group (n=12) and a Vitamin group (n=12). The protein group was given 23 g/d of protein (whey, soybean, BCAA) for 8 weeks and the Vitamin group 23 g/d of vitamin (B, C, D, E and mixed minerals such as calcium, magnesium, zinc) for 8 weeks. All participants had their body composition such as height, weight, skeletal muscle mass, body mass index, and body fat percentage, measured using bioelectrical impedance analysis (BIA) and physical function assessed using grip strength and the short physical performance battery (SPPB). Results : At the end of the intervention, there was a significant increase in skeletal muscle mass (p<.01) in the Protein group (p=.002, 4.92 %) compared to the baseline: it increased by 2.33 %. The Vitamin group had a significant increase in body fat percentage after the intervention (p=.001, 15.35 %) compared to the baseline: body fat percentage decreased by 4.49 %. There were no significant differences in left and right Grip strength/Weight, SPPB, 4-m gait speed, chair stand test, and sense of balance in both groups. Conclusion : The findings from this study suggest that 8 weeks of protein intake have a significant effect on skeletal muscle mass and body fat percentage. Protein intake helped promoting the health of the elderly in rural community during the COVID-19 pandemic. It will assist creating a foundation for providing customized nutrition for the elderly in rural community in the future.

• BMB Reports
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• v.37 no.2
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• pp.159-166
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• 2004

Angiostatin is a potent anti-angiogenic protein. To examine the angiostatin-interacting proteins, we used the display-cloning method with a T7 phage library presenting human cDNAs. The specific T7 phage clone that bound to the immobilized angiostatin was isolated, and a novel gene encoding the displayed polypeptide on the isolated T7 phage was identified. The displayed angiostatin-binding sequence was expressed in E. coli as a soluble protein and purified to homogeneity. This novel angiostatin-binding region interacted specifically to angiostatin with a dissociation constant of $3.4{\times}10^{-7}\;M$. A sequence analysis showed that the identified sequence was a part of the large ORF of 1,998 amino acids, whose function has not yet been characterized. A Northern analysis indicated that the gene containing the angiostatin-binding sequence was expressed differentially in the developmental stages or cell types.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2005.09a
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• pp.379-382
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• 2005

We demonstrate workflows in biological data retrieval and analysis using the DDBJ Web Service; specifically introduce a workflow for the analysis of proteins or proteomics data sets. The workflow mechanically extracts the gene whose protein structure and function are known from all the genes of a human genome in Ensembl (http://www.ensembl.org/) based on cross-references among Ensembl, Swiss-Prot (http://www.ebi.ac.uk/swissprot) and PDB (Protein Data Bank; http://www.wwpdb.org/). The workflow discovered ‘hidden’ linkages among databases. We will be able to integrate distributed and heterogeneous data systems into workflows, if they are provided based on standards for Web services.

• BMB Reports
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• v.46 no.2
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• pp.65-72
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• 2013

In situ detection of RNAs is becoming increasingly important for analysis of gene expression within and between intact cells in tissues. International genomics efforts are now cataloging patterns of RNA transcription that play roles in cell function, differentiation, and disease formation, and they are demon-strating the importance of coding and noncoding RNA transcripts in these processes. However, these techniques typically provide ensemble averages of transcription across many cells. In situ hybridization-based analysis methods complement these studies by providing information about how expression levels change between cells within normal and diseased tissues, and they provide information about the localization of transcripts within cells, which is important in understanding mechanisms of gene regulation. Multi-color, single-molecule fluorescence in situ hybridization (smFISH) is particularly useful since it enables analysis of several different transcripts simultaneously. Combining smFISH with immunofluorescent protein detection provides additional information about the association between transcription level, cellular localization, and protein expression in individual cells.

• Molecules and Cells
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• v.19 no.1
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• pp.23-30
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• 2005

Spinocerebellar ataxia type 1 (SCA1) is an autosomal-dominant neurodegenerative disorder caused by expansion of the polyglutamine tract in the SCA1 gene product, ataxin-1. Using d2EGFP, a short-lived enhanced green fluorescent protein, we investigated whether polyglutamine-expanded ataxin-1 affects the function of the proteasome, a cellular multicatalytic protease that degrades most misfolded proteins and regulatory proteins. In Western blot analysis and immunofluorescence experiments, d2EGFP was less degraded in HEK 293T cells transfected with ataxin-1(82Q) than in cells transfected with lacZ or empty vector controls. To test whether the stability of the d2EGFP protein was due to aggregation of ataxin-1, we constructed a plasmid carrying $ataxin-1-{\Delta}114$, lacking the self-association region (SAR), and examined degradation of the d2EGFP. Both the level of $ataxin-1-{\Delta}114$ aggregates and the amount of d2EGFP were drastically reduced in cells containing $ataxin-1-{\Delta}114$. Furthermore, d2EGFP localization experiments showed that polyglutamine-expanded ataxin-1 inhibited the general function of the proteasome activity. Taken together, these results demonstrate that polyglutamine-expanded ataxin-1 decreases the activity of the proteasome, implying that a disturbance in the ubiquitin-proteasome pathway is directly involved in the development of spinocerebellar ataxia type1.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.60 no.1
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• pp.33-40
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• 2015

Soybean is very useful crop to supply vegetable protein for human. Supply of soybean is increased because it has useful ingredient. Recently, cultivation of soybean in paddy field is increasing due to the increase of rice stockpile in Korea. Hence, in this study, expression of protein was identified regarding different environment for cultivation to investigate the effect of different environment on protein expression. Two-dimensional electrophoresis was performed to investigate the expression of protein using image analysis program to measure degree of protein expression in numerical value. Hannam-kong, Beakcheon-Kong, Hwangkeum-Kong, and Danwon-Kong were used as plant material. 2-DE combined with image analysis revealed that each degree of protein expression of Hannam-Kong and Hwangkeum-Kong in upland field was higher than degree of protein expression in paddy field. However, in case of Beackcheon-Kong, the phenomenon was opposite. In Danwon-kong, the degree of protein expression was not different between up-land field and paddy field. To this end, major protein spots were not different between paddy field and upland field among all cultivars. It could be suggested that protein expression is not severely different by various environment, but different environment affects degree of protein expression.

• Journal of IKEEE
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• v.13 no.3
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• pp.18-23
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• 2009

FEATURE is a computational method to recognize functional and structural sites for automatic protein function prediction. By profiling physicochemical properties around residues, FEATURE can characterize and predict functional and structural sites in 3D protein structures in a high-throughput manner. Despite its effectiveness, it has been challenging to apply FEATURE to novel protein data due to limited customization support. To address this problem, we thoroughly analyze the internal modules of FEATURE and propose a methodology to customize FEATURE so that it can be used for new protein data for automatic functional annotations.