• 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.

• 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.

• 한국환경농학회지
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• 제25권4호
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• pp.371-381
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• 2006

New proteomic techniques have been pioneered extensively in recent years, enabling the high-throughput and systematic analyses of cellular proteins in combination with bioinformatic tools. Furthermore, the development of such novel proteomic techniques facilitates the elucidation of the functions of proteins under stress or disease conditions, resulting in the discovery of biomarkers for responses to environmental stimuli. The ultimate objective of proteomics is targeted toward the entire proteome of life, subcellular localization biochemical activities, and the regulation thereof. Comprehensive analysis strategies of proteomics can be classified into three categories: (i) protein separation via 2-dimensional gel electrophoresis (2-DE) or liquid chromatography (LC), (ii) protein identification via either Edman sequencing or mass spectrometry (MS), and (iii) proteome quantitation. Currently, MS-based proteomics techniques have shifted from qualitative proteome analysis via 2-DE or 2D-LC coupled with off-line matrix assisted laser desorption ionization (MALDI) and on-line electrospray ionization (ESI) MS, respectively, toward quantitative proteome analysis. In vitro quantitative proteomic techniques include differential gel electrophoresis with fluorescence dyes. protein-labeling tagging with isotope-coded affinity tags, and peptide-labeling tagging with isobaric tags for relative and absolute quantitation. In addition, stable isotope-labeled amino acids can be in vivo labeled into live culture cells via metabolic incorporation. MS-based proteomics techniques extend to the detection of the phosphopeptide mapping of biologically crucial proteins, which ale associated with post-translational modification. These complementary proteomic techniques contribute to our current understanding of the manner in which life responds to differing environment.

• Journal of Plant Biotechnology
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• 제37권2호
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• pp.196-204
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• 2010

With the completion of genome sequencing of several organisms, attention has been focused to determine the function and functional network of proteins by proteome analysis. The recent techniques of proteomics have been advanced quickly so that the high-throughput and systematic analyses of cellular proteins are enabled in combination with bioinformatics tools. Furthermore, the development of proteomic techniques helps to elucidate the functions of proteins under stress or diseased condition, resulting in the discovery of biomarkers responsible for the biological stimuli. Ultimate goal of proteomics orients toward the entire proteome of life, subcellular localization, biochemical activities, and their regulation. Comprehensive analysis strategies of proteomics can be classified as three categories: (i) protein separation by 2-dimensional gel electrophoresis (2-DE) or liquid chromatography (LC), (ii) protein identification by either Edman sequencing or mass spectrometry (MS), and (iii) quanitation of proteome. Currently MS-based proteomics turns shiftly from qualitative proteome analysis by 2-DE or 2D-LC coupled with off-line matrix assisted laser desorption ionization (MALDI) and on-line electrospray ionization (ESI) MS, respectively, to quantitative proteome analysis. Some new techniques which include top-down mass spectrometry and tandem affinity purification have emerged. The in vitro quantitative proteomic techniques include differential gel electrophoresis with fluorescence dyes, protein-labeling tagging with isotope-coded affinity tag, and peptide-labeling tagging with isobaric tags for relative and absolute quantitation. In addition, stable isotope labeled amino acid can be in vivo labeled into live culture cells through metabolic incorporation. MS-based proteomics extends to detect the phosphopeptide mapping of biologically crucial protein known as one of post-translational modification. These complementary proteomic techniques contribute to not only the understanding of basic biological function but also the application to the applied sciences for industry.

• 한국정보과학회논문지:소프트웨어및응용
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• 제34권10호
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• pp.889-899
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• 2007

최근 프로테오믹스 분야에서 단백질의 추출, 분리기술의 발전과 고성능 질량분석 장비로 인하여 대량으로, 또 빠르게 샘플을 분석하는 것이 가능해짐에 따라서, 한번의 실험으로부터 얻어지는 실험데이타의 양이 대폭 늘어나게 되었다. 따라서 대량의 데이타를 어떻게 처리하여 필요한 정보만을 얻어내는가가 큰 이슈가 되고 있다. 하지만 기존의 데이타 해석과정은 불필요하게 계산자원을 낭비하는 요소를 상당 부분을 포함하고 있고, 이로 인해 데이타 해석 시간이 증가함은 물론, 종종 옳지 않은 해석 결과를 생성함으로써 결과에 대한 신뢰도의 저하를 초래했다. 본 논문에서는 기존의 데이타 해석 과정에서의 문제점을 지적하고, 데이타 처리의 효율을 높임과 동시에 해석 결과의 신뢰도를 제고하기 위한 SIFTER 시스템을 제안한다. SIFTER 시스템은 본격적인 데이타 해석에 앞서, 질량 스펙트럼의 질을 평가하고 하전량을 결정하는 소프트웨어를 제공한다. 탠덤 질량 스펙트럼에 나타나는 단편 이온의 특성을 고려하여 스펙트럼의 질과 하전량을 정확하게 결정하는 방법을 제공함으로써, 데이타 해석에 앞서 스펙트럼의 질이 낮아 해석이 불가능할 것이 분명한 경우 이들을 미리 제거하고 스펙트럼 해석과정에 잘못된 정보가 사용되지 않도록 한다. 결과적으로 데이타 해석과정에서의 효율과 해석결과의 정확성에 있어 대폭적인 개선을 기대할 수 있다.

• 한국동물번식학회:학술대회논문집
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• 한국동물번식학회 2004년도 춘계학술발표대회
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• pp.173-175
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• 2004

단백질체(Proteome)이란 말은 어원적으로 단백질(protein)에 전체란 뜻을 가진 어미(-body, -some)가 연결된 합성어로 주어진 순간에 세포나 조직이 발현하는 모든 단백질의 총체를 의미하고 이를 연구하는 학문은 Proteomics라 일컫는다. 2001년 2월 International Human Genome Project에 의해 human genome sequence가 밝혀짐으로써 유전체 연구는 일단락 완성되었지만, 염기서열만 가지고는 이 유전자 산물의 기능을 알 수 없었고, 이것이 전사되고 최종적으로 완벽한 모양이 갖추어진 단백질을 분석해야만 그 기능을 알 수 있었다. (중략)

• 대한방사선방어학회:학술대회논문집
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• 대한방사선방어학회 2010년도 춘계 학술발표회 및 심포지엄
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• pp.122-123
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• 2010

• 대한생식의학회:학술대회논문집
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• 대한불임학회 2006년도 제51차 추계학술대회
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• pp.117-117
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• 2006

• Molecules and Cells
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• 제28권4호
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• pp.383-388
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• 2009

The dehydration responsive element binding protein 2C (DREB2C) is a dehydration responsive element/C-repeat (DRE/CRT)-motif binding transcription factor that induced by mild heat stress. Previous experiments established that overexpression of DREB2C cDNA driven by the cauliflower mosaic virus 35S promoter (35S:DREB2C) resulted in increased heat tolerance in Arabidopsis. We first analyzed the proteomic profiles in wild-type and 35S:DREB2C plants at a normal temperature ($22^{\circ}C$), but could not detect any differences between the proteomes of wild-type and 35S: DREB2C plants. The transcript level of DREB2C in 35S: DREB2C plants after treatment with mild heat stress was increased more than two times compared with expression in 35S:DREB2C plants under unstressed condition. A proteomic approach was used to decipher the molecular mechanisms underlying thermotolerance in 35S:DREB2C Arabidopsis plants. Eleven protein spots were identified as being differentially regulated in 35S:DREB2C plants. Moreover, in silico motif analysis showed that peptidyl-prolyl isomerase ROC4, glutathione transferase 8, pyridoxal biosynthesis protein PDX1, and elongation factor Tu contained one or more DRE/CRT motifs. To our knowledge, this study is the first to identify possible targets of DREB2C transcription factors at the protein level. The proteomic results were in agreement with transcriptional data.

• Journal of Microbiology and Biotechnology
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• 제29권11호
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• pp.1817-1829
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• 2019

Porcine deltacoronavirus (PDCoV) is an emerging swine enteric coronavirus that causes diarrhea in neonatal piglets. Like other coronaviruses, PDCoV encodes at least three accessory or species-specific proteins; however, the biological roles of these proteins in PDCoV replication remain undetermined. As a first step toward understanding the biology of the PDCoV accessory proteins, we established a stable porcine cell line constitutively expressing the PDCoV NS7 protein in order to investigate the functional characteristics of NS7 for viral replication. Confocal microscopy and subcellular fractionation revealed that the NS7 protein was extensively distributed in the mitochondria. Proteomic analysis was then conducted to assess the expression dynamics of the host proteins in the PDCoV NS7-expressing cells. High-resolution two-dimensional gel electrophoresis initially identified 48 protein spots which were differentially expressed in the presence of NS7. Seven of these spots, including two up-regulated and five down-regulated protein spots, showed statistically significant alterations, and were selected for subsequent protein identification. The affected cellular proteins identified in this study were classified into functional groups involved in various cellular processes such as cytoskeleton networks and cell communication, metabolism, and protein biosynthesis. A substantial down-regulation of α-actinin-4 was confirmed in NS7-expressing and PDCoV-infected cells. These proteomic data will provide insights into the understanding of specific cellular responses to the accessory protein during PDCoV infection.