• Mass Spectrometry Letters
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• 제12권3호
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• pp.76-80
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• 2021

Scrub typhus is an acute febrile disease caused by the pathogenic bacterium Orientia tsutsugamushi, belonging to the Rickettsiaceae family. The shotgun proteomic analysis was performed using the sera of scrub typhus patients to identify the proteins having their origin in O. tsutsugamushi. Three different databases approaches were used for the identification of the proteomes. We identified the RsmD, an RNA methyltransferase as the commonly detected protein from all three approaches. This protein was not detected in the sera of healthy negative controls. We believe that this protein is a potential biomarker of Orientia tsutsugamushi present in the sera of scrub typhus patients.

• 한국미생물학회:학술대회논문집
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• 한국미생물학회 2006년도 International Meeting of the Microbiological Society of Korea
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• pp.74-75
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• 2006

• BMB Reports
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• 제48권1호
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• pp.19-24
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• 2015

A mouse homozygous for the spontaneous mutation uncovered (Uncv) has a hairless phenotype. A 309-bp non-frameshift deletion mutation in the N-terminal cytoplasmic domain of iRhom2 was identified in Uncv mice ($iRhom2^{Uncv}$) using target region sequencing. The detailed molecular basis for how the iRhom2 mutation causes the hairless phenotype observed in the homozygous $iRhom2^{Uncv}$ mouse remains unknown. To identify differentially expressed proteins in the skin of wild-type and homozygous $iRhom2^{Uncv}$ littermates at postnatal day 5, proteomic approaches, including two-dimensional gel electrophoresis and mass spectrometry were used. Twelve proteins were differentially expressed in the skin in a comparison between wild-type and homozygous $iRhom2^{Uncv}$ mice. A selection of the proteomic results were tested and verified using qRT-PCR, western blot and immunohistochemistry. These data indicate that differentially expressed proteins, especially KRT73, MEMO1 and Coro-1, might participate in the mechanism by which iRhom2 regulates the development of murine skin.

• 대한약침학회지
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• 제9권2호
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• pp.5-16
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• 2006

Objective : It has long been known about the osteogenic effect of CPC-HAS on bone tissues. However, it has not been determined the effect of CPC-HAS on cancer cells. The purpose of this study is to screen the CPC-HAS mediated differentially expressed genes in cancer cells such as HepG2 hepatoma cells. Oligonucleotide microarray and proteomics approaches were employed to screen the differential expression genes. Methods : CPC-HAS was prepared by boiling and stored at $-70^{\circ}C$ until use. Cells were treated with various concentrations of CPC-HAS (0.1, 0.5, 1.5, 10, 20mg/ml) for 24 h. Cell toxicity was tested by MTT assay. To screen the differentially expressed genes in cancer cells, cells were treated with 1.5mg/ml of CPC-HAS. For oligonucleotide microarray assay, total RNA was used for gene expression analysis using oligonucleotide Genechip(Human genome Ul33 Plus 2.0., Affimatrix Co.). For proteomic analysis, total protein was analyzed by 2D gel electrophoresis and Q-TOF mass spectrometer. Results : It has no cytotoxic effects on both HepG2 cell in all concentrations(0.l, 0.5, 1.5, 10, 20mg/ml). In oligonucleotide microarray assay, the number of more than twofold differentially regulated known genes was 23 with 5 up-regulated and 18 down-regulated genes in HepG2 cells. In proteomic analysis, three spots were identified by 2D-gel electrophoresis and Q-TOF analysis. Two down-regulated proteins were aldehyde dehydrogenase 1 and enolase 1, and up-regulated protein was fatty acid binding protein 1 by 1.5mg/ml of CPC-HAS. Discussion : This study showed the screening of CPC-HAS mediated differentially regulated genes using combined approaches of oligonucleotide microarray and proteomic analysis. The screened genes will be used for the better understanding of the therapeutic effects of CPC-HAS on cancer fields.

• Journal of Plant Biotechnology
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• 제41권1호
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• pp.1-9
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• 2014

So far it has been generally considered that proteomic approaches are very useful for studying plant-microbes interaction. In this review, recent studies based on papers published from 2010 to 2013 have investigated proteomics analysis in various interaction during plant-fungal pathogen infection by means of gel-based proteomics coupled with mass spectrometry (MS)-based analysis. In rice, three papers focused on rice-Magnaporthe oryzae interaction were mainly reviewed in this study. Interestingly, another study showed proteomic changes in rice inoculated with Puccinia triticina, which is not only an fungal pathogen in wheat and but also results to the disease resistance with non-host defense manner in rice. Additionally, proteomics analysis has been widely subjected to understand defense mechanism during other crops (wheat, tomato, strawberry and mint) and their fungal pathogen interaction. Crops inoculated are analyzed to identify differentially regulated proteins at various tissues such as leaf and apoplast using 2-DE analysis coupled with various MS approaches such as MALDI-TOF MS, nESI-LC-MS/MS and MudPIT, respectively. Taken together, this review article shows that proteomics is applicable to various organisms to understand plant-fungal pathogen interaction and will contribute to provide important information for crop disease diagnosis and crop protection.

• Bioinformatics and Biosystems
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• 제1권2호
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• pp.95-98
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• 2006

Recent proteomic studies of protein domains require high-throughput and systematic approaches. Since most experiments using protein domains, the modules of protein-protein interactions, require gene cloning, the first experimental step should be retrieving DNA sequences of domain encoding regions from databases. For a large scale proteomic research, however, it is a laborious task to extract a large number of domain sequences manually from several inter-linked databases. We present a new methodology to retrieve DNA sequences of domain encoding regions through automatic database cross-referencing. To extract protein domain encoding regions, it traverses several inter-connected database with validation process. And we applied this method to retrieve all the EGF domain encoding DNA sequences of homo sapiens. This new algorithm was implemented using Python library PAMIE, which enables to cross-reference across distinct databases automatically.

• Asian Pacific Journal of Cancer Prevention
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• 제13권7호
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• pp.3265-3270
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• 2012

Clinically, elevated cancer antigen 125 (CA-125) in blood predicts tumor burden in a woman's body, especially in the ovary, but cannot differentiate between malignant or benign. We here used intensive modern proteomic approaches to identify predictive proteins in the serum of women with elevated CA-125 to differentiate malignant from benign ovarian tumors. We identified differentially expressed proteins in serum samples of ovarian cancer (OC) patients, benign ovarian tumor (BT) patients, and healthy control women using mass spectrometry-based quantitative proteomics. Both the OC and BT patients had elevated CA-125. Quantitation was achieved using isobaric tags for relative and absolute quantitation. We obtained 124 quantified differential serum proteins in OC compared with BT. Two proteins, apolipoprotein A-4 (APOA4) and natural resistance-associated macrophage 1, were verified using Western blotting. Proteome profiling applied to OC cases identified several differential serum proteins in the serum of women with elevated CA-125. A novel protein, APOA4, has the potential to be a marker for malignant tumor differentiation in the serum of women with elevated CA-125.

• Animal cells and systems
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• 제7권3호
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• pp.213-219
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• 2003

The response of plants to pathogens and wounding is dependent upon very sensitive perception mechanisms. Although genetic approaches have revealed a variety of resistance genes that activate common defense responses, defense-related proteins are not well characterized in plants. Therefore, we used a proteomic approach to determine which defense-related proteins are induced by salicylic acid (SA) and wounding in Chinese cabbage. We found that SA and wounding induce pathogenesis-related protein 1a (PR1a) at both protein and mRNA levels using proteomics and Northern blot analysis, respectively. This indicates that our proteomic approach is useful for identifying defense-related proteins. We also identified several other proteins that are induced by SA or wounding. Among the seven SA-induced proteins identified, four may be defense-related, including defense-related protein, phospholipase D (PLD), resistance protein RPS2 homolog, and L-ascorbate peroxidase. Out of the six wounding-induced proteins identified, three may be defense-related: heat shock cognate protein 70 (HSC70), polygalacturonase, and peroxidase P7. The precise functions of these proteins in plant defense responses await further study. However, identification of the defense-related proteins described in this study should allow us to better understand the mechanisms and signal transduction pathways involved in defense responses in Chinese cabbage.

• Mass Spectrometry Letters
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• 제15권2호
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• pp.69 -78
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• 2024

The advancement of high-throughput omics technologies and systems biology is essential for understanding complex biological mechanisms and diseases. The integration of proteomics and metabolomics provides comprehensive insights into cellular functions and disease pathology, driven by developments in mass spectrometry (MS) technologies, including electrospray ionization (ESI). These advancements are crucial for interpreting biological systems effectively. However, integrating these technologies poses challenges. Compared to genomic, proteomics and metabolomics have limitations in throughput, and data integration. This review examines developments in MS equipped electrospray ionization (ESI), and their importance in the effective interpretation of biological mechanisms. The review also discusses developments in sample preparation, such as Simultaneous Metabolite, Protein, Lipid Extraction (SIMPLEX), analytical techniques, and data analysis, highlighting the application of these technologies in the study of cancer or Huntington's disease, underscoring the potential for personalized medicine and diagnostic accuracy. Efforts by the Clinical Proteomic Tumor Analysis Consortium (CPTAC) and integrative data analysis methods such as O2PLS and OnPLS extract statistical similarities between metabolomic and proteomic data. System modeling techniques that mathematically explain and predict system responses are also covered. This practical application also shows significant improvements in cancer research, diagnostic accuracy and therapeutic targeting for diseases like pancreatic ductal adenocarcinoma, non-small cell lung cancer, and Huntington's disease. These approaches enable researchers to develop standardized protocols, and interoperable software and databases, expanding multi-omics research application in clinical practice.

• 한국발생생물학회지:발생과생식
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• 제8권1호
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• pp.1-9
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• 2004

프로테오믹스(proteomics, 단백질체학이라고도 함)의 잠재적 중요성은 간질환, 심장질환, 몇몇 종류의 암 등의 의학, 생식 독성, 발생 독성, 생체 독성 연구 분야에서도 명백하게 제시되었다. 그러나 단백질을 대상으로 연구하여 유전자 기능을 연구하는 프로테오믹스 연구를 각각의 분야에 접목시키려는 노력은 아직까지 빈약하다. 프로테오믹스는 기능을 갖는 단백질들의 발현을 종합적이고 정량적으로 측정하는 가장 직접적인 수단이고, 질병, 약물투여, 쇼크, 내분비계 장애물질 등 생물학적인 동요(perturbation)에 의하여 변하는 단백질들의 발현 양상 변화를 정확하게 관찰할 수 있게 한다. 그리고 생체내 유전자 발현의 궁극적인 양상을 규명할 수 있으며, 또한 유전자, 단백질 및 질병간의 연결고리를 제공한다. 기존의 biomarker는 다른 질병 표지자와 연관성이 높아 직접적인 biomaker와 정확한 연관을 판정하기 어렵다. 따라서 대량 발굴 탐색(high-throughput screening)이 가능한 2차원 전기 영동 분석과 MALDI-TOF또는 protein chip array와 SELDI-TOF에 의한 단백질 분자 구조 분석 기술 및 이들을 지원하는 생물정보학(bioinformatics)의 발전을 이용하여, 생식학 연구에 이용할 수 있는 표적 단백질 발굴 및 정성 정량적 연구에 적절한 이용이 가능할 것이다. 이러한 연구는 생식과정 중 배아 발생 및 조직 기관 발생 중 유전자 발현의 변화, 내분비계 장애물질 등 호르몬 및 독성 물질의 작용 기전, ecotoxicogenomics지표 marker의 변동 분석, 중간대사물질체학(metabolomics)에의 이용 등등의 연구에 필수적인 방법으로 발전할 것이다.