• Journal of KIISE:Databases
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• v.30 no.6
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• pp.573-584
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• 2003

Recent massive data generation by genomics and proteomics requires bioinformatic tools to extract the biological meaning from the massive results. Here we introduce ROSPath, a database system to deal with information on reactive oxygen species (ROS)-mediated cell signaling pathways. It provides a structured repository for handling pathway related data and tools for querying, displaying, and analyzing pathways. ROSPath data model provides the extensibility for representing incomplete knowledge and the accessibility for linking the existing biochemical databases via the Internet. For flexibility and efficient retrieval, hierarchically structured data model is defined by using the object-oriented model. There are two major data types in ROSPath data model: ‘bio entity’ and ‘interaction’. Bio entity represents a single biochemical entity: a protein or protein state involved in ROS cell-signaling pathways. Interaction, characterized by a list of inputs and outputs, describes various types of relationship among bio entities. Typical interactions are protein state transitions, chemical reactions, and protein-protein interactions. A complex network can be constructed from ROSPath data model and thus provides a foundation for describing and analyzing various biochemical processes.

• The KIPS Transactions:PartD
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• v.15D no.5
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• pp.681-690
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• 2008

In proteomics research, the identification of differentially expressed proteins observed under specific conditions is one of key issues. There are several ways to detect the change of a specific protein's expression level such as statistical analysis and graphical visualization. However, it is quiet difficult to handle the spot information of an individual protein manually by these methods, because there are a considerable number of proteins in a tissue sample. In this paper, using database and data mining techniques, the application plan of OLAP data cube and Discovery-driven exploration is proposed. By using data cubes, it is possible to analyze the relationship between proteins and relevant clinical information as well as analyzing the differentially expressed proteins by disease. We propose the measure and exception indicators which are suitable to analyzing protein expression level changes are proposed. In addition, we proposed the reducing method of calculating InExp in Discovery-driven exploration. We also evaluate the utility and effectiveness of the data cube and Discovery-driven exploration in the lung cancer 2-DE gel image.

• Childhood Kidney Diseases
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• v.13 no.2
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• pp.170-175
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• 2009

Purpose : FSGS do not respond well to any kind of therapy and gradually progress to end-stage renal disease. This study was conducted to investigate the difference of protein expression between MCNS and FSGS as a preliminary study for understanding the pathophysiology of FSGS. Methods : Renal biopsy samples of MCNS and FSGS were obtained, which was diagnosed by one pathologist. They were solubilized with a conventional extraction buffer for protein extraction. The solution was applied on immobilized linear gradient strip gel (pH 4-7) using IPGphor system. Silver staining was carried out according to standard method. Protein identification was done by searching NCBI database using MASCOT Peptide Mass Fingerprint software. Results : The differences in protein expressions between MCNS and FSGS were shown by increased or decreased protein spots. Most prominently expressed spot among several spots in FSGS was isolated and analyzed, one of which was glutathione S-transferase (GST) P1-1, whereas it was not found in MCNS. So GSTP1-1 was considered as the one of the key biomarkers in pathogenesis of FSGS. Conclusion : This result would be helpful in diagnosing FSGS and researching FSGS. Further studies for glutathione S-transferase P1-1 might be necessary to elucidate the mechanisms regarding FSGS.

• Tuberculosis and Respiratory Diseases
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• v.61 no.1
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• pp.41-45
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• 2006

Background; Several clinical scoring systems are currently being used to predict the outcome of sepsis, but they all have certain limitations. Therefore, we sought to identify the proteomic biomarkers, with wsing proteomic tools, that differed according to the outcome of sepsis patients. Methods; Upon admission to the ICU, blood samples were obtained from the 16 patients with sepsis who were enrolled in this study. Surface-enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI -TOF MS) was used to identify the markers that could predict the outcome of sepsis. Results; We found six peaks, by using cation and anion chips, that statistically differed between those patients who died and those who survived. Conclusion; The biomarkers we found by using proteomic tools may help predict the prognosis and also plan the treatment of sepsis.

• Development and Reproduction
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• v.8 no.1
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• pp.1-9
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• 2004

The potential importance of proteomic approaches has been clearly demonstrated in other fields of human medical research, including liver and heart disease and certain forms of cancer. However, reproductive researches have been applied to proteomics poorly. Proteomics can be defined as the systematic analysis of proteins for their identity, quantity, and function. It could increase the predictability of early drug development and identify non-invasive biomarkers of toxicity or efficacy. Proteome analysis is most commonly accomplished by the combination of two-dimensional gel electrophoresis(2DE) and MALDI-TOF(matrix-assisted laser desorption ionization-time of flight) MS(mass spectrometry) or protein chip array and SELDI-TOF(surface-enhanced laser desorption ionization-time of flight) MS. In addition understanding the possessing knowledge of the developing biomarkers used to assess reproductive biology will also be essential components relevant to the topic of reproduction. The continued integration of proteomic and genomic data will have a fundamental impact on our understanding of the normal functioning of cells and organisms and will give insights into complex cellular processes and disease and provides new opportunities for the development of diagnostics and therapeutics. The challenge to researchers in the field of reproduction is to harness this new technology as well as others that are available to a greater extent than at present as they have considerable potential to greatly improve our understanding of the molecular aspects of reproduction both in health and disease.

• Journal of Life Science
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• v.20 no.2
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• pp.153-160
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• 2010

This study was conducted to examine the utilization of immunohistochemistry using the bovine anti-brucella immunoglobulin G (IgG) antibody in the diagnosis of brucellosis and to develop a functional biomarker relation for the progress of the disease. Anti-brucella IgG antibody was purified from the affected bovine serum using an affinity chromatography. We performed our investigation on 17 cases of brucellosis and 19 control cases with negative Rose-Bengal test results. Our purified anti-brucella IgG antibody showed a positive immunoreactivity in cytoplasmic hepatocytes of the centrilobular region, and glomeruli and tubular epithelium of the kidney. The protein pattern of the affected liver versus control was analyzed by two-dimensional electrophoresis, showing a different expression pattern of proteins between the two. Five protein spots were up-regulated and another were five down-regulated in the brucellosis liver. Significant upregulaton of catalase and 3-hydroxyacyl-CoA dehydrogenase might be due to a compensatory reaction in response to the endotoxic shock of brucella. In conclusion, the anti-brucella IgG antibody may be a good tool for discriminative diagnosis of the affected tissues and proteomics data suggest new target proteins underlying a possible pathogenic mechanism of brucellosis.

• Journal of Life Science
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• v.33 no.2
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• pp.208-215
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• 2023

In recent decades, the field of aging research has progressed from the genetic and cellular levels to in vivo models of blood exchange. Since genes capable of extending the lifespan in C. elegance have been reported, various potential target molecules have been discovered through genomics, proteomics, metabolomics, and transcriptomics. Accordingly, research on the interactions between target molecules has also been increasing. The parabiosis method, in which two experimental animals are surgically combined, was introduced, and a factor that could reverse the aging phenomenon was discovered using this method. The parabiosis method is used to find more accurate and effective aging-reversal factors that could exist in young blood. As more new evidence has been revealed, the parabiosis method has established a new paradigm for aging research. Moreover, a device capable of exchanging blood elaborately in laboratory animals was published in 2022 and presented new results necessary for aging reversal. Since GDF11, was reported, many other anti-aging candidates that are soluble factors in blood, such as β2m, TIMP2, VCAM1, Gpld1, and clusterin, have been discovered. In addition, mcicroglia cells and neuroinflammation have been directly proven to be aging factors. These latest research results were obtained by parabiosis, the newly designed device for plasmapheresis, and injecting young blood or conditioned blood methods. In this review, we discuss the latest research results using the device and young blood administration in old mice.