• Genomics & Informatics
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• 제4권1호
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• pp.1-10
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• 2006

Epigenetic alterations are common features of human solid tumors, though global DNA methylation has been difficult to assess. Restriction Landmark Genomic Scanning (RLGS) is one of technology to examine epigenetic alterations at several thousand Notl sites of promoter regions in tumor genome. To assess sequence information for Notl sequences in RLGS gel, we cloned 1,161 unique Notl-linked clones, compromising about 60% of the spots in the soluble region of RLGS profile, and performed BLAT searches on the UCSC genome server, May 2004 Freeze. 1,023 (88%) unique sequences were matched to the CpG islands of human genome showing a large bias of RLGS toward identifying potential genes or CpG islands. The cloned Notl-loci had a high frequency (71%) of occurrence within CpG islands near the 5' ends of known genes rather than within CpG islands near the 3' ends or intragenic regions, making RLGS a potent tool for the identification of gene-associated methylation events. By mixing RLGS gels with all Notl-linked clones, we addressed 151 Notl sequences onto a standard RLGS gel and compared them with previous reports from several types of tumors. We hope our sequence information will be useful to identify novel epigenetic targets in any types of tumor genome.

• Asian-Australasian Journal of Animal Sciences
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• 제20권11호
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• pp.1662-1669
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• 2007

The high mobility group AT-hook1 (HMGA1) proteins are known to be related to the regulation of gene transcription, replication and promotion of metastatic progression in cancer cells. The loss of expression by disrupting the HMGA1 gene affects insulin signaling and causes diabetes in the mouse. Previously identified single nucleotide polymorphism (SNP) of HMGA1 was significantly associated with fat deposition traits in the pig. In this study, we identified 3,935 bp nucleotide sequences from exon 5 to exon 8 of the bovine HMGA1 gene and its mRNA expression was observed by quantitative real-time PCR. Six single nucleotide polymorphisms in the bovine HMGA1 gene were detected and the allele frequencies of these SNPs were investigated using the PCR-RFLP method in nine cattle breeds including Limousin, Simmental, Brown Swiss, Hereford, Angus, Charolais, Hanwoo, Brahman and Red Chittagong cattle. The map location showed that the bovine HMGA1 gene was also closely located with a previously identified meat quality QTL region indicating this gene is the most likely positional candidate for meat quality traits in cattle.

• Molecular & Cellular Toxicology
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• 제4권1호
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• pp.78-84
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• 2008

EGFR has been intensively investigated as a target to block the signal transduction pathway which stimulates cancer growth and metastasis. Studies about structure-activity relationship for tricyclic azepine derivatives were performed with topomer-CoMFA. The derived topomer-CoMFA model with steric and electrostatic field parameters based on fragment units gave reasonable statistics ($q^2$=0.561, $r^2$=0.679). The model explains why a halogen atom at the meta position of aniline is important to increases inhibitory activity. This comes from an electrostatically negative groups are favored near this region. The model also shows that there are sterically favored regions around methoxy group extended from oxazepine derivatives. The findings about steric and electrostatic effects can be utilized for designing new inhibitors.

• 대한한의학방제학회지
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• 제28권4호
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• pp.313-325
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• 2020

Objectives : To explore the associated potential pathways and molecular targets of Hwangryunhaedok-tang(HHT) by the approaches of network pharmacology and bioinformatics in traditional chinese medicine(TCM). Methods : Hwangryunhaedok-tang constituent drugs(Coptidis Rhizoma, CR; Scutellariae Radix, SR; Phellodendri Cortex, PC; Gardeniae Fructus, GF) and their processing types were searched from TCM systems pharmacology(TCMSP). The databases of TCMSP, Kyoto Encyclopedia of Genes and Genomes(KEGG), MCODE and STRING were used to gather information. The network of bioactive ingredients and target gene was constructed by Cytoscape software(version 3.8). Results : A total of 94 HHT active compounds(CR, 12; SR, 35; PC, 33; GF, 14, respectively) were found, and HHT were identified by TCMSP. Applications of KEGG and MCODE analysis indicates that total of 6 bioactive ingredients in the top 10% ranking were obtained and 32 diseases of HHT were screened. The molecular pathway analysis revealed that HHT exerts cancer, inflammation and cerebrovascular diseases effects by acting on several signaling pathway. In addition, HHT found that three genes(e.g. SPIN1, TRIM25, and APP) correlate with the aforementioned diseases. Conclusions : This study showed that network pharmacology analysis is useful to elucidate the complex mechanisms of action of HHT.

• Biomolecules & Therapeutics
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• 제26권4호
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• pp.409-416
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• 2018

Vasicinone, a quinazoline alkaloid from Adhatoda vasica Nees. is well known for its bronchodilator activity. However its anti-proliferative activities is yet to be elucidated. Here-in we investigated the anti-proliferative effect of vasicinone and its underlying mechanism against A549 lung carcinoma cells. The A549 cells upon treatment with various doses of vasicinone (10, 30, 50, $70{\mu}M$) for 72 h showed significant decrease in cell viability. Vasicinone treatment also showed DNA fragmentation, LDH leakage, and disruption of mitochondrial potential, and lower wound healing ability in A549 cells. The Annexin V/PI staining showed disrupted plasma membrane integrity and permeability of PI in treated cells. Moreover vasicinone treatment also lead to down regulation of Bcl-2, Fas death receptor and up regulation of PARP, BAD and cytochrome c, suggesting the anti-proliferative nature of vasicinone which mediated apoptosis through both Fas death receptors as well as Bcl-2 regulated signaling. Furthermore, our preliminary studies with vasicinone treatment also showed to lower the ROS levels in A549 cells and have potential free radical scavenging (DPPH, Hydroxyl) activity and ferric reducing power in cell free systems. Thus combining all, vasicinone may be used to develop a new therapeutic agent against oxidative stress induced lung cancer.

• Journal of Microbiology and Biotechnology
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• 제19권7호
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• pp.635-646
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• 2009

Rapid and accurate diagnosis of diseases is very important for appropriate treatment of patients. Recent advances in molecular-level interaction and detection technologies are upgrading the clinical diagnostics by providing new ways of diagnosis, with higher speed and accuracy. In particular, DNA microarrays can be efficiently used in clinical diagnostics which span from discovery of diseaserelevant genes to diagnosis using its biomarkers. Diagnostic DNA microarrays have been used for genotyping and determination of disease-relevant genes or agents causing diseases, mutation analysis, screening of single nucleotide polymorphisms (SNPs), detection of chromosome abnormalities, and global determination of posttranslational modification. The performance of DNA-microarray-based diagnosis is continuously improving by the integration of other tools. Thus, DNA microarrays will play a central role in clinical diagnostics and will become a gold standard method for disease diagnosis. In this paper, various applications of DNA microarrays in disease diagnosis are reviewed. Special effort was made to cover the information disclosed in the patents so that recent trends and missing applications can be revealed.

• Molecular & Cellular Toxicology
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• 제2권2호
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• pp.141-149
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• 2006

Tamoxifen (TAM), a non-steroidal anti estrogen anticancer drug and chemopreventive agent for breast cancer, have caused cholestasis in liver. The potent hepatocarcinogenicity of this drug has been reported. Methotrexate (MTX) is dihydrofolate reductase inhibitor which interfaces with the synthesis for urine nucleotide and dTMP. And it may cause atrophy, necrosis and steatosis in liver. These two anticancer drug have well-known hepatotoxicity. So, in this study we compare the gene expression pattern of antitumor agent TAM and MTX, using the cDNA microarray. We have used 4.8 K cDNA microarray to identify hepatotoxicity-related genes in 5-week-old male Sprague-Dawley (SD) rats. Confirm the pattern of gene expression, we have used Real time PCR for targeted gene. In the case of MTX, Protease related gene (Ctse, Ctsk) and Protein kinase (Pctk 1) have shown specific expression pattern. And in the case of TAM, apoptosis related gene (Pdcd 8) and signal transduction related gene (kdr) have significantly up regulated during treatment time. Gene related with growth factor, lipid synthesis, chemokins were significantly changed. From the result of this study, the information about influence of TAM and MTX to hepatoxicity will provide.

• Molecules and Cells
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• 제41권9호
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• pp.853-867
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• 2018

As the most common type of endocrine malignancy, papillary thyroid cancer (PTC) accounts for 85-90% of all thyroid cancers. In this study, we presented the hypothesis that SDC4 gene silencing could effectively attenuate epithelial mesenchymal transition (EMT), and promote cell apoptosis via the $Wnt/{\beta}-catenin$ signaling pathway in human PTC cells. Bioinformatics methods were employed to screen the determined differential expression levels of SDC4 in PTC and adjacent normal samples. PTC tissues and adjacent normal tissues were prepared and their respective levels of SDC4 protein positive expression, in addition to the mRNA and protein levels of SDC4, $Wnt/{\beta}-catenin$ signaling pathway, EMT and apoptosis related genes were all detected accordingly. Flow cytometry was applied in order to detect cell cycle entry and apoptosis. Finally, analyses of PTC migration and invasion abilities were assessed by using a Transwell assay and scratch test. In PTC tissues, activated $Wnt/{\beta}-catenin$ signaling pathway, increased EMT and repressed cell apoptosis were determined. Moreover, the PTC K1 and TPC-1 cell lines exhibiting the highest SDC4 expression were selected for further experiments. In vitro experiments revealed that SDC4 gene silencing could suppress cell migration, invasion and EMT, while acting to promote the apoptosis of PTC cells by inhibiting the activation of the $Wnt/{\beta}-catenin$ signaling pathway. Besides, $si-{\beta}-catenin$ was observed to inhibit the promotion of PTC cell migration and invasion caused by SDC4 overexpression. Our study revealed that SDC4 gene silencing represses EMT, and enhances cell apoptosis by suppressing the activation of the $Wnt/{\beta}-catenin$ signaling pathway in human PTC.

• Interdisciplinary Bio Central
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• 제3권4호
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• pp.15.1-15.11
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• 2011

Background: Histone deacetylase (HDAC) 8 is one of its family members catalyzes the removal of acetyl groups from N-terminal lysine residues of histone proteins thereby restricts transcription factors from being expressed. Inhibition of HDAC8 has become an emerging and effective anti-cancer therapy for various cancers. Application computational methodologies may result in identifying the key components that can be used in developing future potent HDAC8 inhibitors. Results: Facilitating the discovery of novel and potential chemical scaffolds as starting points in the future HDAC8 inhibitor design, quantitative structure-activity relationship models were generated with 30 training set compounds using genetic function approximation (GFA) and Bayesian algorithms. Six GFA models were selected based on the significant statistical parameters calculated during model development. A Bayesian model using fingerprints was developed with a receiver operating characteristic curve cross-validation value of 0.902. An external test set of 54 diverse compounds was used in validating the models. Conclusions: Finally two out of six models based on their predictive ability over the test set compounds were selected as final GFA models. The Bayesian model has displayed a high classifying ability with the same test set compounds and the positively and negatively contributing molecular fingerprints were also unveiled by the model. The effectively contributing physicochemical properties and molecular fingerprints from a set of known HDAC8 inhibitors were identified and can be used in designing future HDAC8 inhibitors.

• Bulletin of the Korean Chemical Society
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• 제33권4호
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• pp.1123-1127
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• 2012

P-gp (P-glycoprotein) is a member of the ATP binding cassette (ABC) family of transporters. It transports many kinds of anticancer drugs out of the cell. It plays a major role as a cause of multidrug resistance (MDR). MDR function may be a cause of the failure of chemotherapy in cancer and influence pharmacokinetic properties of many drugs. Hence classification of candidate drugs as substrates or nonsubstrate of the P-gp is important in drug development. Therefore to identify whether a compound is a P-gp substrate or not, in silico method is promising. Recursive Partitioning (RP) method was explored for prediction of P-gp substrate. A set of 261 compounds, including 146 substrates and 115 nonsubstrates of P-gp, was used to training and validation. Using molecular descriptors that we can interpret their own meaning, we have established two models for prediction of P-gp substrates. In the first model, we chose only 6 descriptors which have simple physical meaning. In the training set, the overall predictability of our model is 78.95%. In case of test set, overall predictability is 69.23%. Second model with 2D and 3D descriptors shows a little better predictability (overall predictability of training set is 79.29%, test set is 79.37%), the second model with 2D and 3D descriptors shows better discriminating power than first model with only 2D descriptors. This approach will be used to reduce the number of compounds required to be run in the P-gp efflux assay.