Browsing by Subject "Drug effect"
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Item Open Access Functionally conserved effects of rapamycin exposure on zebrafish(Spandidos Publications, 2016-03) Sucularli, C.; Shehwana, H.; Kuscu, C.; Dungul, D. C.; Ozdag, H.; Konu, O.Mechanistic target of rapamycin (mTOR) is a conserved serine/threonine kinase important in cell proliferation, growth and protein translation. Rapamycin, a well-known anti-cancer agent and immunosuppressant drug, inhibits mTOR activity in different taxa including zebrafish. In the present study, the effect of rapamycin exposure on the transcriptome of a zebrafish fibroblast cell line, ZF4, was investigated. Microarray analysis demonstrated that rapamycin treatment modulated a large set of genes with varying functions including protein synthesis, assembly of mitochondrial and proteasomal machinery, cell cycle, metabolism and oxidative phosphorylation in ZF4 cells. A mild however, coordinated reduction in the expression of proteasomal and mitochondrial ribosomal subunits was detected, while the expression of numerous ribosomal subunits increased. Meta-analysis of heterogeneous mouse rapamycin microarray datasets enabled the comparison of zebrafish and mouse pathways modulated by rapamycin, using Kyoto Encyclopedia of Genes and Genomes and Gene Ontology pathway analysis. The analyses demonstrated a high degree of functional conservation between zebrafish and mice in response to rapamycin. In addition, rapamycin treatment resulted in a marked dose-dependent reduction in body size and pigmentation in zebrafish embryos. The present study is the first, to the best of our knowledge, to evaluate the conservation of rapamycin-modulated functional pathways between zebrafish and mice, in addition to the dose-dependent growth curves of zebrafish embryos upon rapamycin exposure.Item Open Access One-step synthesis of size-tunable Ag nanoparticles incorporated in electrospun PVA/cyclodextrin nanofibers(Pergamon Press, 2014) Celebioglu A.; Aytac Z.; Umu, O. C. O.; Dana, A.; Tekinay, T.; Uyar, TamerOne-step synthesis of size-tunable silver nanoparticles (Ag-NP) incorporated into electrospun nanofibers was achieved. Initially, in situ reduction of silver salt (AgNO3) to Ag-NP was carried out in aqueous solution of polyvinyl alcohol (PVA). Here, PVA was used as reducing agent and stabilizing polymer as well as electrospinning polymeric matrix for the fabrication of PVA/Ag-NP nanofibers. Afterwards, hydroxypropyl-beta-cyclodextrin (HPβCD) was used as an additional reducing and stabilizing agent in order to control size and uniform dispersion of Ag-NP. The size of Ag-NP was ∼8 nm and some Ag-NP aggregates were observed for PVA/Ag-NP nanofibers, conversely, the size of Ag-NP decreased from ∼8 nm down to ∼2 nm within the fiber matrix without aggregation were attained for PVA/HPβCD nanofibers. The PVA/Ag-NP and PVA/HPβCD/Ag-NP nanofibers exhibited surface enhanced Raman scattering (SERS) effect. Moreover, antibacterial properties of PVA/Ag-NP and PVA/HPβCD/Ag-NP nanofibrous mats were tested against Gram-negative (Escherichia coli) and Gram-positive (Staphylococcus aureus) bacteria.Item Open Access Theoretical analysis of substituent effects on building blocks of conducting polymers: 3, 4'-substituted bithiophenes(American Chemical Society, 1999) Salzner, U.; Kızıltepe, T.Substituents are widely used to modify the properties of conducting polymers. To study substituent effects on energy levels and energy gaps systematically, CH3-, OH-, NH2-, CN-, and CCH-substituted bithiophenes were examined with density functional theory and NBO analysis. Total charges and :r-electron densities were analyzed separately to examine π- and σ-effects. Second-order perturbation theory was used to quantify conjugation in terms of orbital interactions. NBO orbital energies were employed to investigate the effect of alternating donor-acceptor substitution. Substituents in 3- and 4- positions shift HOMO and LUMO levels in parallel and hardly influence HOMO- LUMO gaps. For level shifting the π-donating and π-accepting abilities are most important; electronegativity mainly influences the σ-orbitals and is less crucial in determining energy gaps. Alternating donor-acceptor substitution leads to HOMO and LUMO energies that are average between those of the parent systems and has little effect on energy gaps.