• Title/Summary/Keyword: protein-protein interaction extraction

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Liquid chromatography-tandem mass spectrometric analysis of oleracone D and its application to pharmacokinetic study in mice

  • Lim, Dong Yu;Lee, Tae Yeon;Lee, Jaehyeok;Song, Im-Sook;Han, Young Taek;Choi, Min-Koo
    • Analytical Science and Technology
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    • v.34 no.5
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    • pp.193-201
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    • 2021
  • We have demonstrated a sensitive analytical method of measuring oleracone D in mouse plasma using a liquid chromatography-tandem mass spectrometry (LC-MS/MS). Oleracone D and oleracone F (internal standard) in mouse plasma samples were processed using a liquid-liquid extraction method with methyl tertbutyl ether, resulting in high and reproducible extraction recovery (80.19-82.49 %). No interfering peaks around the peak elution time of oleracone D and oleracone F were observed. The standard calibration curves for oleracone D ranged from 0.5 to 100 ng/mL and were linear with r2 of 0.992. The inter- and intra-day accuracy and precision and the stability fell within the acceptance criteria. The pharmacokinetics of oleracone D following intravenous and oral administration of oleracone D at doses of 5 mg/kg and 30 mg/kg, respectively, were investigated. When oleracone D was intravenously injected, it had first-order elimination kinetics with high clearance and volume of distribution values. The absolute oral bioavailability of this compound was calculated as 0.95 %, with multi-exponential kinetics. The low aqueous solubility and a high oral dose of oleracone D may explain the different elimination kinetics of oleracone D between intravenous and oral administration. Collectively, this newly developed sensitive LC-MS/MS method of oleracone D could be successfully utilized for investigating the pharmacokinetic properties of this compound and could be used in future studies for the lead optimization and biopharmaceutic investigation of oleracone D.

Reconstruction and Exploratory Analysis of mTORC1 Signaling Pathway and Its Applications to Various Diseases Using Network-Based Approach

  • Buddham, Richa;Chauhan, Sweety;Narad, Priyanka;Mathur, Puniti
    • Journal of Microbiology and Biotechnology
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    • v.32 no.3
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    • pp.365-377
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    • 2022
  • Mammalian target of rapamycin (mTOR) is a serine-threonine kinase member of the cellular phosphatidylinositol 3-kinase (PI3K) pathway, which is involved in multiple biological functions by transcriptional and translational control. mTOR is a downstream mediator in the PI3K/Akt signaling pathway and plays a critical role in cell survival. In cancer, this pathway can be activated by membrane receptors, including the HER (or ErbB) family of growth factor receptors, the insulin-like growth factor receptor, and the estrogen receptor. In the present work, we congregated an electronic network of mTORC1 built on an assembly of data using natural language processing, consisting of 470 edges (activations/interactions and/or inhibitions) and 206 nodes representing genes/proteins, using the Cytoscape 3.6.0 editor and its plugins for analysis. The experimental design included the extraction of gene expression data related to five distinct types of cancers, namely, pancreatic ductal adenocarcinoma, hepatic cirrhosis, cervical cancer, glioblastoma, and anaplastic thyroid cancer from Gene Expression Omnibus (NCBI GEO) followed by pre-processing and normalization of the data using R & Bioconductor. ExprEssence plugin was used for network condensation to identify differentially expressed genes across the gene expression samples. Gene Ontology (GO) analysis was performed to find out the over-represented GO terms in the network. In addition, pathway enrichment and functional module analysis of the protein-protein interaction (PPI) network were also conducted. Our results indicated NOTCH1, NOTCH3, FLCN, SOD1, SOD2, NF1, and TLR4 as upregulated proteins in different cancer types highlighting their role in cancer progression. The MCODE analysis identified gene clusters for each cancer type with MYC, PCNA, PARP1, IDH1, FGF10, PTEN, and CCND1 as hub genes with high connectivity. MYC for cervical cancer, IDH1 for hepatic cirrhosis, MGMT for glioblastoma and CCND1 for anaplastic thyroid cancer were identified as genes with prognostic importance using survival analysis.

Anti-oxidant and Anti-aging Effect of Extracts from Seed of Camellia japonica L. by Supercritical Fluid Extraction (한국산 동백종자 초임계 추출물의 피부 항산화 및 항노화 연구)

  • Kim, Hee-Taek;Kim, Tae-Jun;Kim, Ee-Hwa;Kwak, Byeong-Mun
    • The Journal of Korean Medicine Ophthalmology and Otolaryngology and Dermatology
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    • v.33 no.4
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    • pp.32-43
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    • 2020
  • Objectives : The aim of this study was to investigate the anti-oxidant and anti-aging effect of the seed of Camellia japonica L. extracted by supercritical CO2. Methods : The cell viability was performed by MTT assay. Nitric oxide (NO) production was performed by NO assay. The anti-oxidant effect was performed by beta-carotene bleaching assay and the intracellular proteome was analyzed expression of each 15 proteins by 2-D electrophoresis. Results : Fatty acid analysis of extract from Camellia japonica L. has shown oleic acid was 84%. And the antioxidant effect was about 186% compared with alpha-tocoperol(0.1%) by beta carotene bleaching assay. In 2D PAGE analysis, fifteen protein changes in five mechanisms which was collagen synthesis pathway, MMPs, ECM-cell interaction, cytokine, antioxidant enzymes were analyzed. Conclusions : On this study extract from seed of Camellia japonica L. by supercritical extraction could be used as a antioxidant and antiaging substance for the skin.

Skin Anti-aging and Anti-wrinkle Effects of Pinus koreaiensis Seed Oil (해송자 오일의 피부 항노화 및 주름 개선 효과)

  • Kim, Hyung-Mook;Kim, Tae-Jun;Im, Dong-bin;Ha, Sun-Bong;Kim, Ee-Hwa;Cha, Byung-Sun;Heo, Hyo-Jin;Brito, Sofia;Lee, Yong-Moon;Bin, Bum-Ho;Kwak, Byeong-Mun
    • The Journal of Korean Medicine Ophthalmology and Otolaryngology and Dermatology
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    • v.34 no.4
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    • pp.1-11
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    • 2021
  • Objectives : The aim of this study was to investigated the anti-aging and anti-wrinkles effects of the pinus koreaiensis seed(PKS) oil. Methods : The anti-oxidant effect was performed by beta-carotene bleaching assay and the intracellular proteome was analyzed expression of each 15 proteins by 2-D electrophoresis. And fatty acid was analysed by gas chromatography. Anti-wrinkle effect was analyzing human skin by the PRIMOS system. Results : Fatty acid analysis of PKS oil has shown oleic acid was 49.7% and linoleic acid was 34.1%. And the antioxidant effect was about 125% compared with alpha-tocoperol(0.1%) by beta carotene bleaching assay. In 2D PAGE analysis, fifteen protein changes in five mechanisms which was collagen synthesis pathway, MMPs, ECM-cell interaction, cytokine, antioxidant enzymes were analyzed. In case of anti-wrinkle effect was proved in vivo by analyzing human skin by the PRIMOS system. The analysis results of eye wrinkles for 4 weeks showed an improvement effect of over 6%. Conclusions : In this study, the amount of protein change in the five mechanism through the cell experiment and the skin anti wrinkle efficacy by the human in vivo test were investigated. As a result pinus koreaiensis seed oil by supercritical extraction could be used as a anti-aging and anti-wrinkle substance for the skin.

Studies on the Myofibrillar Proteins Part 2. New Procedure for Extraction of Regulatory Proteins from Myofibrils (근원섬유단백질에 관한 연구 (제2보) 근수축 조절단백질의 새로운 정제방법)

  • Yang, Ryung;Kim, Chul-Jai;Yu, Ju-Hyun;Lee, Hyuk-Sin;Cho, Young-Dong
    • Korean Journal of Food Science and Technology
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    • v.6 no.4
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    • pp.199-208
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    • 1974
  • An attempt was made to study on new method for the extraction of the regulatory proteins from myofibrils, and the procedures for the preparation of desensitized actomyosin and for complete extraction of troponin-tropomyosin complex were developed. When myofibrils were treated through the procedures developed in this study, actomyosin obtained had no Ca-sensitivity, indicating that Ca-sensitizing protein factor had been removed completely from myofibril. Consequently, it was concluded that the procedures developed in this study were convenient to test whether Ca-sensitizing proteins has been removed or not. When Mg-activated ATPase activity of myofibril were measured, the myofibrillar ATPase turned into the actomyosin type ATPase with the progress of the treatment. This result was interpreted to show that the regulatory proteins of the myofibril seems to play a cementing role on the structure of myofibril. When supernatant containing the regulatory proteins were fractionated with $(NH_4)_2SO_4$ saturation solution, regulatory proteins, ${\alpha}-actinin$ and troponia-tropomyosin complex, could be obtained and they showed their typical phyoislogical activity which modify the actin-myosin interaction. The amount of troponin-tropomyosin complex in myofibril was 72 mg per g myofibril. This result was in good agreement with the results reported by many investigators, and therefore it was concluded that our procedures for the extraction of troponin-tropomyosin complex were desirable to study on the quantitative analysis of troponin-tropomyosin complex.

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