• Journal of KIISE:Computer Systems and Theory
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• v.34 no.10
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• pp.474-492
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• 2007

In the protein interaction network, there are many meaningful functional modules, each involving several protein interactions to perform discrete functions. Pathways and protein complexes are the examples of the functional modules. In this paper, we propose a new method for detecting the functional modules based on concept. A conceptual functional module, briefly concept module is introduced to match the modules taking them as its instances. It is defined by the corresponding rule composed of triples and operators between the triples. The triples represent conceptual relations reifying the protein interactions of a module, and the operators specify the structure of the module with the relations. Furthermore, users can define a composite concept module by the counterpart rule which, in turn, is defined in terms of the predefined rules. The concept module makes it possible to detect functional modules that are conceptually similar as well as structurally identical to users' queries. The rules are managed in the XML format so that they can be easily applied to other networks of different species. In this paper, we also provide a visualized environment for intuitionally describing complexly structured rules.

• Journal of Veterinary Clinics
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• v.20 no.4
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• pp.431-436
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• 2003

The purpose of this study is to evaluate urine protein-to-creatinine ratio as a parameter for early detection of nephrotic syndrome and as a parameter for monitoring effectiveness in early course of treatment. Nine healthy dogs were sensitized by intravenous injection with 1 $\mu$g of endotoxin and 5 mg of native bovine serum albumin. After 1 week, 120 mg of cationized bovine serum albumin was injected intravenously 5 times a week. Among nine dogs, five dogs were confirmed as having developed glomerulonephritis and nephrotic syndrome by increase of urine protein-to-creatinine ratio(>1.0), hypoalbuminemia (<1.5 g/dl), hypercholesterolemia (> 240 mg/dl) and azotemia (BUN>40 mg/dl). During the induction of glomerulonephritis and the progression to nephrotic syndrome, the increase of urine protein-to-creatinine ratio was firstly detected. 1 to 4 weeks later, hypoalbuminemia, hypercholesterolemia, and azotemia were detected. Prednisolone (2.2 mg/kg, bid) was administered orally to the dogs with induced nephrotic syndrome. In early stage of treatment, the increase of serum albumin and decrease of serum cholesterol were detected. 1 to 4 weeks later, decrease of urine protein-to-creatinine ratio was detected. It was concluded that urine protein-to-creatinine ratio is a useful parameter for early detection of nephrotic syndrome, and serum albumin and cholesterol are useful parameters for the monitoring in early course of treatment in nephrotic syndrome.

• Journal of Veterinary Science
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• v.23 no.4
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• pp.55.1-55.12
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• 2022

Background: ASF was first reported in Kenya in 1910 in 1921. In China, ASF spread to 31 provinces including Henan and Jiangsu within six months after it was first reported on August 3, 2018. The epidemic almost affected the whole China, causing direct economic losses of tens of billions of yuan. Cause great loss to our pig industry. As ELISA is cheap and easy to operate, OIE regards it as the preferred serological method for ASF detection. P54 protein has good antigenicity and is an ideal antigen for detection. Objective: To identify a conservative site in the African swine fever virus (ASFV) p54 protein and perform a Cloth-enzyme-linked immunosorbent assay (ELISA) for detecting the ASFV antibody in order to reduce risks posed by using the live virus in diagnostic assays. Method: We used bioinformatics methods to predict the antigen epitope of the ASFV p54 protein in combination with the antigenic index and artificially synthesized the predicted antigen epitope peptides. Using ASFV-positive serum and specific monoclonal antibodies (mAbs), we performed indirect ELISA and blocking ELISA to verify the immunological properties of the predicted epitope polypeptide. Results: The results of our prediction revealed that the possible antigen epitope regions were A23-29, A36-45, A72-94, A114-120, A124-130, and A137-150. The indirect ELISA showed that the peptides A23-29, A36-45, A72-94, A114-120, and A137-150 have good antigenicity. Moreover, the A36-45 polypeptide can react specifically with the mAb secreted by hybridoma cells, and its binding site contains a minimum number of essential amino acids in the sequence 37DIQFINPY44. Conclusions: Our study confirmed a conservative antigenic site in the ASFV p54 protein and its amino acid sequence. A competitive ELISA method for detecting ASFV antibodies was established based on recombinant p54 and matching mAb. Moreover, testing the protein sequence alignment verified that the method can theoretically detect antibodies produced by pigs affected by nearly all ASFVs worldwide.

• Toxicological Research
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• v.17
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• pp.59-69
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• 2001

Arsenic exposure is associated with several human diseases, including cancers, atherosclerosis, hypertension, and cerebrovascular diseases. In cultured cells, arsenite, an inorganic arsenic com-pound, was demonstrated to interfere with many physiological functions, such as enhancement of oxidative stress, delay of cell cycle progression, and induction of structural and numerical changes of chromosomes. The objective of this study is to investigate the effects of arsenic exposure on gene expression profiles by colorimetric cDNA microarray technique. HFW (normal human diploid skin fibroblasts), CL3 (human lung adenocarcinoma cell line), and HaCaT (immortalized human keratinocyte cell line) were treated with 5 $\mu\textrm{M}$ or 10 $\mu\textrm{M}$ sodium arsenite for 6 or 16 h, respectively. By a dual-color detection system, the expression profile of arsenite-treated cultures was compared to that of control cultures. Several genes expressed differentially were identified on the microarray membranes. For example, MDM2, SWI/SNF, ubiquitin specific protease 4, MAP3K11, RecQ protein-like 5, and Ribosomal protein Ll0a were consistently induced in all three cell types by arsenite, whereas prohibitin, cyclin D1, nucleolar protein 1, PCNA, Nm23, and immediate early protein (ETR101) were apparently inhibited. The present results suggest that arsenite insults altered the expression of several genes participating in cellular responses to DNA damage, stress, transcription, and cell cycle arrest.

• The Korean Journal of Physiology and Pharmacology
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• v.8 no.6
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• pp.345-349
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• 2004

Heat shock ($43^{\circ}C$ for 60 minutes) is sufficient to induce apoptosis in a wide number of cell lines. In this study, we asked whether DNA strand breaks are responsible for this phenomenon. Using the highly sensitive comet assay for DNA damage detection, we were unable to demonstrate DNA breaks immediately after heat shock in Raji human Iymphoid cells. It showed that DNA breaks were not necessary for hyperthermic apoptosis, since its activity is indicative of DNA lesions. Here, we present a suggestion that a protein(s) is the major target for heat shock apoptosis. We firstly found glycerol, which reportedly stabilizes protein structure, showed a protective effect in Raji cells against hyperthermic apoptosis. In addition, quercetin, which modulates transcription of the heat shock protein family members, enhanced apoptotic death induced by hyperthermia. Furthermore, Raji cells are protected by a pre-mild heat treatment prior to the killing dose of heat shock.

• Proceedings of the Korean Society of Applied Pharmacology
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• 1994.11a
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• pp.143-145
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• 1994

Chimeric fusion proteins involving IgG have proven valuable in studying protein-protein interactions and may possess therapeutic applications as well. For example, three receptor subtypes for the natriuretic peptides, when fused to the Fc portion of human IgG ${\gamma}$ chain, were quantitatively and qualitatively indistinguishable from the native receptor, thus allowing detailed structure-function studies of the receptor. In an attempt to block human immunodeficiency virus infectivity with soluble derivatives of CD4, a CD4/IgG Fc chimeric molecule was shown to increase the plasma half life of soluble CD4 and possessed the added advantage of IgG Fc-mediated placental transfer. In the case of the KGFR, this approach provided a framework for dissection of its ligand binding domains and made it possible to demonstrate that high affinity binding sites for two ligands, aFGF and KGF, reside within different receptor Ig-like domains. Chimeric molecules fused to immunoglobulins would have the advantages of secretion from transfected cells as well as detection and purification from medium utilizing Staphylococcus aureus Protein A. In addition, where highly related receptors make their discrimination very hard due to the difficulties in generating specific immunochemical probes, IgG fusion protein with tailor-made specificities confers particular advantages to elucidate patterns of receptor distribution and expression. The approach described here may have general applications in defining ligand-receptor interactions as well as searching for specific agonists and antagonists of receptor function.

• Asian Pacific Journal of Cancer Prevention
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• v.13 no.5
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• pp.1911-1915
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• 2012

Aim: New technologies for the early detection of pancreatic cancer (PC) are urgently needed. The aim of the present study was to screen for the potential protein biomarkers in serum using proteomic fingerprint technology. Methods: Magnetic beads combined with surface-enhanced laser desorption/ionization (SELDI) TOF MS were used to profile and compare the protein spectra of serum samples from 85 patients with pancreatic cancer, 50 patients with acute-on-chronic pancreatitis and 98 healthy blood donors. Proteomic patterns associated with pancreatic cancer were identified with Biomarker Patterns Software. Results: A total of 37 differential m/z peaks were identified that were related to PC (P < 0.01). A tree model of biomarkers was constructed with the software based on the three biomarkers (7762 Da, 8560 Da, 11654 Da), this showing excellent separation between pancreatic cancer and non-cancer., with a sensitivity of 93.3% and a specificity of 95.6%. Blind test data showed a sensitivity of 88% and a specificity of 91.4%. Conclusions: The results suggested that serum biomarkers for pancreatic cancer can be detected using SELDI-TOF-MS combined with magnetic beads. Application of combined biomarkers may provide a powerful and reliable diagnostic method for pancreatic cancer with a high sensitivity and specificity.

• Korean Journal of Veterinary Research
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• v.36 no.3
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• pp.615-619
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• 1996

Sera of pigs with clinically normal and infectious conditions were analyzed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis(SDS-PAGE) to demonstrate the specific changes in protein profile. In the sera from pigs with infection, haptoglobin with a 40KDa protein was found to be increased as compared to that of sera from normal pigs. As a rapid detection method for monitoring infections at large-scale farms, one of acute phase protein, haptoglobin, was selected to compare the concentrations between infectious and non-infectious conditions. Haptoglobin concentrations were low in pigs with clinically normal conditions but significantly increased in pigs with Aujesky's disease, hog cholera and parvo-virus infection. The studies provide that haptoglobin can be used as an indicator to monitor infections early at farm level.

• Korean Journal of Veterinary Service
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• v.34 no.1
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• pp.1-4
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• 2011

A surface plasmon resonance imaging (SPRI) assay was developed for measuring porcine circovirus type 2 (PCV2) antibody using a recombinant capsid protein as an antigen. The diagnostic potential of SPRI for detecting antibodies to the PCV2 capsid protein was compared with that of a conventional enzyme-linked immunosorbent assay (ELISA) using 70 pig serum samples taken from 6 pig farms. There was a strong positive correlation between the SPRI and ELISA (n = 70, r = 0.911, P<0.01). Therefore, this recombinant capsid protein can be used as an antigen for serological studies, and the SPRI, a label-free and high-throughput method, is expected to be a valuable tool in the serodiagnosis of PCV2 infection.

• 한국정보컨버전스학회:학술대회논문집
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• 2008.06a
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• pp.39-42
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• 2008

G protein-coupled receptor(GPCR) family is a cell membrane protein, and plays an important role in a signaling mechanism which transmits external signals through cell membranes into cells. Now, it is estimated that there may be about 800-1000 GPCRs in a human genome. But, GPCRs each are known to have various complex control mechanisms and very unique signaling mechanisms. GPCRs are involved in maintaining homeostasis of various human systems including an endocrine system or a neural system and thus, disorders in activity control of GPCRs are thought to be the major source of cardiovascular disorders, metabolic disorders, degenerative disorders, carcinogenesis and the like. As more than 60% of currently marketed therapeutic agents target GPCRs, the GPCR field has been actively explored in the pharmaceutical industry. Structural features, and class and subfamily of GPCRs are well known by function, and accordingly, the most fundamental work in studies identifying the previous GPCRs is to classify the GPCRs with given protein sequences. Studies for classifying previously identified GPCRs more easily with mathematical models have been mainly going on. Considering that secondary sequences of proteins, namely, secondary binding structures of amino acids constituting proteins are closely related to functions, the present paper does not place the focus on primary sequences of proteins as previously practiced, but instead, proposes a method to transform primary sequences into secondary structures and compare the secondary structures, and then detect an unknown GPCR assumed to have a same function in databases of previously identified GPCRs.