• Mass Spectrometry Letters
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• 제5권1호
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• pp.16-23
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• 2014

Liquid chromatography based mass spectrometry (LC-MS) is a key technology for analyzing highly complex and dynamic proteome samples. With highly accurate and sensitive LC-MS analysis of complex proteome samples, efficient data processing is another critical issue to obtain more information from LC-MS data. A typical proteomic data processing starts with protein database search engine which assigns peptide sequences to MS/MS spectra and finds proteins. Although several search engines, such as SEQUEST and MASCOT, have been widely used, there is no unique standard way to interpret MS/MS spectra of peptides. Each search engine has pros and cons depending on types of mass spectrometers and physicochemical properties of peptides. In this study, we describe a novel data process pipeline which identifies more peptides and proteins by correcting precursor ion mass numbers and unifying multi search engines results. The pipeline utilizes two open-source software, iPE-MMR for mass number correction, and iProphet to combine several search results. The integrated pipeline identified 25% more proteins in mouse epididymal adipose tissue compared with the conventional method. Also the pipeline was validated using control and colitis induced colon tissue. The results of the present study shows that the integrated pipeline can efficiently identify increased number of proteins compared to the conventional method which can be a breakthrough in identification of a potential biomarker candidate.

• Genomics & Informatics
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• 제2권2호
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• pp.75-80
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• 2004

In a variety of animal species, the perinatal exposure of experimental animals to the 2,3,7,8-tetrachlorodibenzo­p-dioxin (TCDD) leads to the immune dysfunction, which is more severe and persistent than that caused by adult exposure. We report here the changes of gene expression and the identification of the marker-genes representing the dioxin exposure. The expressions of the transcripts were analyzed using the 11 K oligonucleotide­microarray from the bone marrow cells of male C57BL/6J mice after an intraperitoneal injection of $1{\mu}g$ TCDD/kg body weight at various time intervals: gestational 6.5 day(G6.5), 13.5 day(G13.5), 18.5 day(G18.5), and postnatal 3 (P3W)and 6 week (P6W). The type of self-organizing maps(SOM) representing the specific exposure dioxin could be identified as follows; G6.5D(C14), G13.5D(C0, C5, C10, C18), G18.5D(7): P3W(C2, C21), and P6W(C4, C15, C20). The candidate marker-genes were restricted to the transcripts, which could be consistently expressed greater than $\pm$2-fold in three experiments. The resulting candidates were 85 genes, the characteristics of that were involved in cell physiology and cell functions such as cell proliferation and immune function. We identified the biomarker-genes for dioxin exposure: smc -like 2 from SOM C14 for the dioxin exposure at G6.5D, focal adhesion kinase and 6 other genes from C0, and protein tyrosine phosphatase 4a2 and 3 other genes from C5 for G13.5D, platelet factor 4 from C7 for G18.5D, fos from C2 for P3W.

• BMB Reports
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• 제41권8호
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• pp.597-603
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• 2008

Atopic dermatitis (AD) is a chronic inflammatory skin disease that induces changes in various inflammatory skin cells. The prevalence of AD is as high as 18% in some regions of the world, and is steadily rising. However, the pathophysiology of AD is poorly understood. To identify the proteins involved in AD pathogenesis, a comparative proteomic analysis of protein expression in peripheral blood mononuclear cells isolated from AD patients and healthy donors was conducted. Significant changes were observed in the expressions of fourteen proteins, including the vinculin, PITPNB, and Filamin A proteins. Among the proteins, $\alpha$-SNAP and FLNA decreased significantly, and PITPNB increased significantly in AD patients compared with control subjects; these findings were further confirmed by real-time PCR and Western blot analysis. The comparative proteome data may provide a valuable clue to further understand AD pathogenesis, and several differentially regulated proteins may be used as biomarkers for diagnosis and as target proteins for the development of novel drugs.

• 생명과학회지
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• 제19권7호
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• pp.866-870
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• 2009

Fascin은 액틴결합 단백질로 형성을 포함한 많은 발생과정에 있어서 중요한 역할을 한다. Fascin은 암세포에 대한 생체표지인자로도 잘 알려져 있다. 그러나 이러한 fascin 유전자의 발현조절기전은 현재까지 잘 알려져있다. 그러나 이러한 fascin 유전자의 발현조절기전은 현재까지 잘 알려져 있지 않다. 본 연구에서는 Raf 돌연변이 초파리에서 이미 보고 되어있는 초파리 fascin 돌연변이 초파리의 휘어진 등털 표현형을 관찰함으로써 초파리 fascin 유전자의 발현이 Raf신호체계에 의해 조절되는 가를 조사하였다. RT-PCR과 Western blot의 실험 방법으로 Raf 유전자 돌연변이 초파리에서 fascin의 발현이 감소되어 있는 것을 확인하였으며, GAL4-UAS계로 Raf를 과발현시킨 초파리에서 fascin 발현이 증가하는 것을 확인할 수 있었다. 또한 세포의 증식과 이동 연구모델계로 잘 알려져 있는 초파리의 혈액세포에서 이러한 조절기전을 확인하였다. 이러한 결과들은 fascin유전자의 발현이 Raf 신호체계에 의해 조절된다는 것을 나타낸다.

• 한국식품영양학회지
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• 제24권1호
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• pp.1-11
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• 2011

This study was designed to investigate the relationships among blood lipid levels, nutrient intakes, oxidation and inflammation markers of overweight adults(23$\leq$BMI<25) and obese(BMI$\geq$25) in Korea. The subjects were classified as control, borderline hyperlipidemia. and hyperlipidemia groups based on The Korean Guidelines of Hyperlipidemia Treatment for the Prevention of Atherosclerosis. The study was conducted through questionnaires, anthropometric checkups, 2-days of 24 hr recalls, and blood biomarker analyses. Systolic blood pressure(SBP) was significantly increased in the hyperlipidemia group(p=0.0464). Intakes of nutrients were not significantly different among the three groups. Blood oxidized-LDL levels were significantly increased in the hyperlipidemia group(p<0.0001). Blood triglyceride(TG) levels were positively associated with BMI(p=0.0498), SBP(p=0.0158), and diastolic blood pressure(DBP; p=0.0076). Blood total cholesterol levels were positively associated with SBP(p=0.0005), and blood HDL-cholesterol levels were negatively associated with body fat (p=0.0408). Blood LDL-cholesterol levels were negatively associated with height(p=0.0207), and blood VLDL-cholesterol levels were positively associated with SBP(p=0.0011) and DBP(p=0.0490). Intakes of protein(p=0.0257) and dietary fiber (p=0.0094) were positively associated with blood HDL-cholesterol levels. Frap levels were positively associated with TG levels(p=0.0001) and VLDL-cholesterol levels(p=0.0077). Oxidized-LDL levels were positively associated with LDL-cholesterol levels(p=0.0135). These results suggest that oxidation and inflammation markers may be related to hypercholesterolemia progress, and dietary fiber intake may play a role in preventing hyperlipidemia in overweight and obese adults.

• Clinical and Experimental Pediatrics
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• 제64권7호
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• pp.347-354
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• 2021

Background: Neutrophil gelatinase-associated lipocalin (NGAL) has emerged as a valuable biomarker of urinary tract infection (UTI) in children. Purpose: This study aimed to compare the diagnostic accuracy of urinary NGAL (uNGAL) with those of serum C-reactive protein (CRP) and white blood cell (WBC) count for predicting UTI and acute pyelonephritis (APN) in febrile children. Methods: The medical charts of children undergoing uNGAL measurements between November 2017 and August 2019 were retrospectively reviewed. Patients with a suspected or diagnosed UTIs were included. The diagnostic accuracies of uNGAL, serum CRP, and WBC count for detecting UTI and APN were investigated. Independent predictors of UTI and APN were investigated using multivariable logistic regression analyses. Results: A total of 321 children were enrolled in this study. The uNGAL levels were higher in the UTI group (n=157) than in the non-UTI group (n=164) (P<0.05). Among children with a UTI, uNGAL levels were higher in the APN group (n=70) than, the non-APN group (n=87) (P<0.05). In the multivariate analysis, uNGAL was independently associated with UTI and APN (both P<0.05). Serum CRP and WBC count were not correlated with the presence of UTI and APN. Receiver operating curve analyses showed that the uNGAL level had the highest area under the curve (AUC) for predicting UTI and APN, respectively (AUC, uNGAL vs. CRP vs. WBC count, 0.860 vs. 0.608 vs. 0.669 for UTI; 0.780 vs. 0.680 vs. 0.639 for APN, all P<0.05, respectively). The predictive values and likelihood ratios of uNGAL were superior to those of serum CRP and WBC count for detecting UTI and APN at each cutoff level. Conclusion: UNGAL may be more useful than serum CRP and WBC count for identifying and assessing UTI in febrile children.

• Journal of Cancer Prevention
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• 제23권4호
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• pp.191-196
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• 2018

Background: Type 2 diabetes mellitus (T2DM) and cancer are serious health problems worldwide, and their prevalences have been on the rise in recent years. It has been reported that adropin plays an important role in the development of T2DM, oxidative stress, inflammation, and obesity. However, there is limited information available on T2DM from human studies, especially for the Korean population. In this study, we aimed to investigate the correlation between adropin levels and obesity of Korean T2DM patients. Methods: Thirty-six T2DM patients were recruited for this study. The participants were further classified into female (n = 12) and male (n = 24). Their body composition, metabolic parameters, inflammatory factors, and oxidative stress were measured. Results: The severity of obesity is more manifested in male than in female. Plasma triglyceride (TG) and high-sensitivity C-reactive protein (hs-CRP) levels of male were significantly higher than female. The plasma adropin and adiponectin level of female was significantly higher than male. The body weight, body mass index (BMI), body fat mass were negatively correlated with the plasma adropin level in female, whereas adropin has positive correlation with adiponectin in female. The hs-CRP was negatively correlated with the plasma adropin level in female and male. malondialdehyde, reactive oxidative species, and $TNF-{\alpha}$ was not significantly correlated with adropin in patients with T2DM. Conclusions: These findings suggest that adropin may be more used as a biomarker for predicting the risk of obesity and inflammation in Korean patients with T2DM, especially women.

• 고신대학교 의과대학 학술지
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• 제33권3호
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• pp.337-346
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• 2018

Objectives: Serum procalcitonin (PCT) is a specific biomarker that rises after bacterial infection, and levels of PCT are known to correlate with the severity and mortality of patients with pneumonia and sepsis. However, the usefulness of PCT levels in acute pyelonephritis is unknown. This study aimed to evaluate the effectiveness of using the PCT level as a predictive test for bacteremia in acute pyelonephritis. Methods: Between January 2012 and June 2013, 140 patients diagnosed with acute pyelonephritis were admitted to Haeundae Paik Hospital. Serum PCT, C-reactive protein (CRP), and white blood cell (WBC) levels at pre- and post- treatment were measured. Blood and urine cultures were obtained from all patients. The levels of PCT, CRP, and WBCs were each compared between the blood culture-positive and blood culture-negative groups to assess their effectiveness in predicting bacteremia. Results: Pre-treatment PCT level was 0.77 ng/mL (95% CI: 0.42-1.60 ng/mL) in the blood culture-negative group and 4.89 ng/mL (95% CI: 2.88-9.04 ng/mL) in the blood culture-positive group, and the increase between the two groups was statistically significant. The area under the receiver operating characteristic curve of PCT level for prediction of bacteremia was 0.728. A cut-off value of 1.23 ng/mL indicated a sensitivity of 79.0 % and specificity of 60.0 % for PCT level. Conclusions: Serum PCT level is a useful predictive test for bacteremia in acute pyelonephritis. Through the early detection of bacteremia, serum PCT level can help estimate the prognosis and predict complications such as sepsis.

• Journal of Microbiology and Biotechnology
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• 제31권7호
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• pp.921-932
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• 2021

LINC01272 is a long non-coding RNA (lncRNA) that has been considered as a biomarker for many diseases including lung squamous cell carcinoma. Here, we investigated the function and mechanism of LINC01272 on lung cancer (LC). The differential expression of LINC01272 in LC and normal samples was analyzed by GEPIA based on the data from TCGA-LUAD database, as survival prognosis was analyzed through Kaplan-Meier Plotter. LINC01272 overexpression plasmid and miR-7-5p mimic were transfected into A549 and PC-9 cells. LINC01272, miR-7-5p and cardiolipin synthase 1 (CRLS1) mRNA expression was measured by quantitative reverse transcription-polymerase chain reaction. Cell viability was detected through MTT assay. Cell multiplication was evaluated by cell formation assay. Cell apoptosis was assessed through flow cytometry assay. Through bioinformatics, the target miRNA of LINC01272 and downstream genes of miR-7-5p were predicted. The targeting relationship was tested by dual luciferase reporter analysis. CRLS1, B-cell lymphoma-2 (Bcl-2), BCL2-associated X (Bax) and cleaved caspase-3 protein levels were detected through western blot. LINC01272 was downregulated in LC and low LINC01272 expression had poor prognosis. In A549 and PC-9 cells, LINC01272 inhibited cell viability and multiplication and induced apoptosis. LINC01272 negatively regulated miR-7-5p and CRLS1 was a target of miR-7-5p. MiR-7-5p reversed the effect of LINC01272 on viability, multiplication, apoptosis and expression of miR-7-5p and CRLS1 as well as apoptosis-related factors (Bcl-2, Bax and cleaved caspase-3). LINC01272 suppressed cell multiplication and induced apoptosis via regulating the miR-7-5p/CRLS1 axis in LC.

• Journal of Periodontal and Implant Science
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• 제52권5호
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• pp.383-393
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• 2022

Purpose: Aloe-emodin (AE), a natural anthraquinone abundant in aloe plants and rhubarb (Rheum rhabarbarum), has long been used to treat chronic inflammatory diseases. However, AE's underlying mechanisms in periodontal inflammation have not been fully elucidated. Acidic mammalian chitinase (AMCase) is a potential biomarker involved in bone remodeling. This study aimed to evaluate AE's effect on periodontitis in rats and investigate AMCase expression. Methods: Eighteen Sprague-Dawley rats were separated into the following groups: healthy (group 1), disease (group 2), vehicle (group 3), AE high-dose (group 4), and AE low-dose (group 5). Porphyromonas gingivalis ligatures were placed in rats (groups 2-5) for 7 days. Groups 4 and 5 were then treated with AE for an additional 14 days. Saliva was collected from all groups, and probing pocket depth was measured in succession. Periodontal pocket tissues were subjected to histomorphometric analysis after the rats were sacrificed. Bone marrow-derived macrophages and murine macrophages were stimulated with receptor activator of nuclear factor-κB ligand (RANKL) and treated with different concentrations of AE. AMCase expression was detected from the analysis of saliva, periodontal pocket tissues, and differentiated osteoclasts. Results: Among rats with P. gingivalis-induced periodontitis, the alveolar bone resorption levels and periodontal pocket depth were significantly reduced after treatment with AE. AMCase protein expression was significantly higher in the disease group than in the healthy control (P<0.05). However, AE inhibited periodontal inflammation by downregulating AMCase expression in saliva and periodontal pocket tissue. AE significantly reduced RANKL-stimulated osteoclastogenesis by modulating AMCase (P<0.05). Conclusions: AE decreases alveolar bone loss and periodontal inflammation, suggesting that this natural anthraquinone has potential value as a novel therapeutic agent against periodontal disease.