Browsing by Subject "Animal cell culture"

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    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.
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    Identification of novel neutralizing single-chain antibodies against vascular endothelial growth factor receptor 2
    (2011) Erdag, B.; Koray Balcioglu, B.; Ozdemir Bahadir, A.; Serhatli, M.; Kacar O.; Bahar, A.; Seker, U.O.S.; Akgun, E.; Ozkan, A.; Kilic, T.; Tamerler, C.; Baysal, K.
    Human vascular endothelial growth factor (VEGF) and its receptor (VEGFR-2/kinase domain receptor [KDR]) play a crucial role in angiogenesis, which makes the VEGFR-2 signaling pathway a major target for therapeutic applications. In this study, a single-chain antibody phage display library was constructed from spleen cells of mice immunized with recombinant human soluble extracellular VEGFR-2/KDR consisting of all seven extracellular domains (sKDR D1-7) to obtain antibodies that block VEGF binding to VEGFR-2. Two specific single-chain antibodies (KDR1.3 and KDR2.6) that recognized human VEGFR-2 were selected; diversity analysis of the clones was performed by BstNI fingerprinting and nucleotide sequencing. The single-chain variable fragments (scFvs) were expressed in soluble form and specificity of interactions between affinity purified scFvs and VEGFR-2 was confirmed by ELISA. Binding of the recombinant antibodies for VEGFR-2 receptors was investigated by surface plasmon resonance spectroscopy. In vitro cell culture assays showed that KDR1.3 and KDR2.6 scFvs significantly suppressed the mitogenic response of human umbilical vein endothelial cells to recombinant human VEGF 165 in a dose-dependent manner, and reduced VEGF-dependent cell proliferation by 60% and 40%, respectively. In vivo analysis of these recombinant antibodies in a rat cornea angiogenesis model revealed that both antibodies suppressed the development of new corneal vessels (p < 0.05). Overall, in vitro and in vivo results disclose strong interactions of KDR1.3 and KDR2.6 scFvs with VEGFR-2. These findings indicate that KDR1.3 and KDR2.6 scFvs are promising antiangiogenic therapeutic agents. © 2011 International Union of Biochemistry and Molecular Biology, Inc.
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    İnsan hareketlerinin PIR-sensör tabanlı bir sistemle sınıflandırılması
    (IEEE, 2008-04) Urfalıoğlu, Onay; Soyer, Emin B.; Töreyin, B. Uğur; Çetin, A. Enis
    Bu bildiride, tek bir pasif kızılberisi sensörü (PIR) kullanarak beş farklı insan hareketi ve bir hareketsiz arkaplan gürültüsünden oluşan toplam 6 çeşit olay için bir sınıflandırma yöntemi önerilmiştir. Otomatik olay sınıflandırma sistemleri, dinamik süreçler barındıran ortamlar için yeni uygulamalara fırsat vermektedir. Olay sınıflandırması, herhangi bir sensör ya da sensör dizisinden gelen işaretlerin analiz edilerek, belirli bir olaya ait dinamik süreçle eşleştirilmesi olarak tanımlanabilir. Genelde, insan etkinliklerinin izlenmesi uygulamalarında kamera ve mikrofonlar kullanılmaktadır. Bir alternatif veya bir tümleyici yaklaşım olarak, bahsi geçen uygulamalarda PIR sensörleri de kullanılabilir. Bu bildiride, olay sınıflandırılması için Bayes yaklaşımına dayalı olan şartlı Gauss karışım modeli (CGMM) kullanımı önerilmektedir. Deneysel çalışmalarda, bu yaklaşımın başarılı olduğu görülmüştür.
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    Texturing of titanium (Ti6Al4V) medical implant surfaces with MHz-repetition-rate femtosecond and picosecond Yb-doped fiber lasers
    (Optical Society of American (OSA), 2011) Erdoǧan, M.; Öktem, B.; Kalaycioǧlu H.; Yavaş, S.; Mukhopadhyay P.K.; Eken, K.; Özgören, K.; Aykaç, Y.; Tazebay, U.H.; Ilday F.O.
    We propose and demonstrate the use of short pulsed fiber lasers in surface texturing using MHz-repetition-rate, microjoule- and sub-microjoule-energy pulses. Texturing of titanium-based (Ti6Al4V) dental implant surfaces is achieved using femtosecond, picosecond and (for comparison) nanosecond pulses with the aim of controlling attachment of human cells onto the surface. Femtosecond and picosecond pulses yield similar results in the creation of micron-scale textures with greatly reduced or no thermal heat effects, whereas nanosecond pulses result in strong thermal effects. Various surface textures are created with excellent uniformity and repeatability on a desired portion of the surface. The effects of the surface texturing on the attachment and proliferation of cells are characterized under cell culture conditions. Our data indicate that picosecond-pulsed laser modification can be utilized effectively in low-cost laser surface engineering of medical implants, where different areas on the surface can be made cell-attachment friendly or hostile through the use of different patterns. © 2011 Optical Society of America.