• 대한치과보철학회:학술대회논문집
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• 대한치과보철학회 2005년도 추계학술대회
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• pp.65-65
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• 2005

• Biotechnology and Bioprocess Engineering:BBE
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• 제9권2호
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• pp.69-75
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• 2004

In recent years, the importance of proteomic works, such as protein expression, detection and identification, has grown in the fields of proteomic and diagnostic research. This is because complete genome sequences of humans, and other organisms, progress as cellular processing and controlling are performed by proteins as well as DNA or RNA. However, conventional I protein analyses are time-consuming; therefore, high throughput protein analysis methods, which allow fast, direct and quantitative detection, are needed. These are so-called protein microarrays or protein chips, which have been developed to fulfill the need for high-throughput protein analyses. Although protein arrays are still in their infancy, technical development in immobilizing proteins in their native conformation on arrays, and the development of more sensitive detection methods, will facilitate the rapid deployment of protein arrays as high-throughput protein assay tools in proteomics and diagnostics. This review summarizes the basic technologies that are needed in the fabrication of protein arrays and their recent applications.

• Molecular & Cellular Toxicology
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• 제3권4호
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• pp.238-245
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• 2007

Chronic formaldehyde inhalation studies have suggested its relativity to teratogenicity, cancer incidence, neurodegenerative and vascular disorders. Many toxicological data on the formaldehyde toxicity are available, but proteomic results showing complete protein profiles are limited. Therefore, alterations of protein expression patterns upon formaldehyde treatment were investigated in the human lung epithelial cell line. Differentially expressed proteins following formaldehyde treatment were analyzed on 2-dimensional gels, and further analyzed by MALDI-TOF to identify the proteins. Among the identified proteins, 24 proteins were notably up-regulated and 6 proteins were down-regulated. In particular, cytoskeleton related protein named vinculin and Rho GDP dissociation inhibitor which plays a key role in apoptosis increased remarkably.

• BMB Reports
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• 제42권7호
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• pp.456-461
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• 2009

Proteomic analyses of differentially expressed proteins in rat retinal ganglion cells (RGC-5) following S-nitrosoglutathione (GSNO), an NO donor, treatment were conducted. Of the approximately 314 protein spots that were detected, 19 were differentially expressed in response to treatment with GSNO. Of these, 14 proteins were up-regulated and 5 were down- regulated. Notably, an increase in GAPDH expression following GSNO treatment was detected in RGC-5 cells through Western blotting as well as proteomics. The increased GAPDH expression in response to GSNO treatment was accompanied by an increase in Herc6 protein, an E3 ubiquitin ligase. Moreover, GSNO treatment resulted in the translocation of GADPH from the cytosol to the nucleus and its subsequent accumulation. These results suggest that NO stress-induced apoptosis may be associated with the nuclear translocation and accumulation of GAPDH in RGC-5 cells.

• 한국생물정보학회:학술대회논문집
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• 한국생물정보시스템생물학회 2005년도 BIOINFO 2005
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• pp.23-28
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• 2005

The high-dimensionality and insufficiency of gene expression profiles and proteomic profiles makes feature selection become a critical step in efficiently building accurate models for cancer problems based on such data sets. In this paper, we use a method, called Discrete Function Learning algorithm, to find discriminatory feature vectors based on information theory. The target feature vectors contain all or most information (in terms of entropy) of the class attribute. Two data sets are selected to validate our approach, one leukemia subtype gene expression data set and one ovarian cancer proteomic data set. The experimental results show that the our method generalizes well when applied to these insufficient and high-dimensional data sets. Furthermore, the obtained classifiers are highly understandable and accurate.

• 한국생물정보학회:학술대회논문집
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• 한국생물정보시스템생물학회 2005년도 BIOINFO 2005
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• pp.331-336
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• 2005

Post translational modifications (PTMs) discovery is an important problem in proteomic. In the past, people discover PTMs by Tandem Mass Spectrometer based on ‘bottom-up’ strategy. However, such strategy suffers from the problem of failing to discover all PTMs. Recently, due to the improvement in proteomic technology, Taylor et al. proposed a database software to discover PTMs with ‘topdown’ strategy by FTMS, which avoids the disadvantages of ‘bottom-up’ approach. However, their proposed algorithm runs in exponential time, requires a database of proteins, and needs prior knowledge about PTM sites. In this paper, a new algorithm is proposed which can work without a protein database and can identify modifications in polynomial time. Besides, no prior knowledge about PTM sites is needed.

• Journal of Microbiology and Biotechnology
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• 제11권6호
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• pp.1111-1114
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• 2001

An extracellular fibrinolytic-enzyme-producing bacterium was isolated from Doen-Jang, a Korean traditional fermented flood, and identified as Bacillus sp. DJ based on its morphology and cellular fatty acid composition. The total extracellular fibrinase (EF) from Bacillus sp. DJ was analyzed using three fibrin zymographic techniques, SDS-fibrin zymography (SDS-FZ), isoelectrofocucing-fibrin zymographs(IEF-FZ), and a two-dimensional SDS-fibrin zymographic analysis (2D SDS-FZ). As a result, the EP map of Bacillus sp. DJ was established. The results suggest that the 2D SDS-FZ method will be a useful tool for the proteomic approach for many other bacterial pretenses.

• Journal of Crop Science and Biotechnology
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• 제11권4호
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• pp.227-232
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• 2008

Drought stress is one of the major abiotic stresses in agriculture worldwide. We report here a proteomic approach to investigate the impact of post-fertilization drought on grain quality in rice seed endosperm (Oryza sativa cv. IR-64). Plants were stressed for 4 days at 3 days before heading. Total proteins of endosperm were extracted and separated by two-dimensional gel electrophoresis. Not many protein spots showed differential accumulation in drought-stressed samples. More than 400 protein spots were reproducibly detected, including three that were up-regulated and five down-regulated. Mass spectrometry analysis and database searching helped us to identify six spots representing different proteins. Functionally, the identified proteins were related to protein synthesis and carbohydrate metabolism, such as Granule-Bound Starch Synthase (GBSS, Wx protein), which is thought to play a very important role in starch biosynthesis and quality, a very crucial factor in determining rice grain quality.

• Journal of Microbiology and Biotechnology
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• 제18권5호
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• pp.968-974
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• 2008

Proteomic analysis led to identification of the proteins of Vibrio vulnificus that were induced upon exposure to INT-407 cells, and 7 of which belong to the functional categories such as amino acid transport/metabolism, nucleotide transport/metabolism, posttranslational modification/protein turnover/chaperones, and translation. Among the genes encoding the host-induced proteins, disruption of purH, trpD, tsaA, and groEL2 resulted in reduced cytotoxicity. The purH, trpD, and tsuA mutants showed impaired growth in the INT-407 lysate; however, the growth rate of the groEL2 mutant was not significantly changed, indicating that the possible roles of the host-induced proteins in the virulence of V. vulnificus are rather versatile.

• Mass Spectrometry Letters
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• 제12권4호
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• pp.163-171
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• 2021

Emiliania huxleyi is a marine phytoplankton that plays a critical role in global carbon and sulfur cycling. The genome of E. huxleyi has been sequenced, and an in-depth proteomic profile of this organism has been reported. This study analyzed the phosphoproteome of E. huxleyi and identified its changes under calcium-limited conditions. A TiO₂ microcolumn was used for phosphopeptide enrichment, followed by liquid chromatography-tandem mass spectrometry analysis. Overall, we identified 7,010 phosphorylated sites on 3,355 phosphopeptides associated with 2,929 phosphoproteins in E. huxleyi. Quantitative analysis revealed changes in the phosphoproteome in E. huxleyi when ambient conditions changed to calcium-limited conditions, notably the phosphorylation of some transporters was altered. This study provides an overview of protein phosphorylation in E. huxleyi and paves the way for further investigations of its biological functions.