Scopus İndeksli Yayınlar Koleksiyonu / Scopus Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/11147/7148
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Conference Object Citation - WoS: 2Citation - Scopus: 1Determination of Aluminum Oxide Thickness on the Annealed Surface of 8000 Series Aluminum Foil by Fourier Transform Infrared Spectroscopy(Springer, 2017) İnanç Uçar, Özlem; Ekin Meşe, Ayten; Birbaşar, Onur; Dündar, Murat; Özdemir, DurmuşAluminum foil produced with prescribed thermomechanical processing route develop oxide film. Alloy chemistry and annealing practices, particularly its duration and exposed temperature, determine the characteristics of the oxide film. The magnitude and characteristics of the oxide film may impair surface features leading to serious problems in some applications, such as coating, printing and in some severe cases failure in formability. Therefore, it is important for the rolling industry to be able to monitor the oxide formation on the foil products and quantify its thickness. Well known methods to measure an oxide thickness that is in the order of nanometer, require meticulous sample preparation techniques, long duration for measurements and sophisticated equipment. However, in this study, a simple and rapid grazing angle attenuated total reflectance infrared (GA-ATR-FTIR) spectroscopic method combined with chemometrics multivariate calibration has been developed for the oxide thickness determination which is validated with x-ray photoelectron spectroscopy (XPS). 3000 and 8000 series aluminum foil materials which were produced by twin roll casting technique were used in this study. Foil samples were annealed at various different temperatures and annealing times in a laboratory scale furnace. Immediately after collecting GA-ATR-FTIR spectra, the 3000 series alloy samples were sent to a laboratory where XPS reference oxide thickness measurements had been performed. Partial Least Squares (PLS) method was used to develop a multivariate calibration model based on FTIR spectra and XPS reference oxide thickness values in order to predict the aluminum oxide thickness. The correlation coefficient of XPS reference oxide thickness values versus grazing angle ATR-FTIR based PLS predicted values was found as 0.9903 the standard error of cross validation (SECV) was found to be 0.29 nm in range of 4.9–14.0 nm for Al2O3. In addition, the standard error of prediction (SEP) for the validation set was 0.24 nm with the model generated with three principal components (PCs). © The Minerals, Metals & Materials Society 2017.Article Citation - WoS: 6Citation - Scopus: 6A Molecular and Biophysical Comparison of Macromolecular Changes in Imatinib-Sensitive and Imatinib-Resistant K562 Cells Exposed To Ponatinib(SAGE Publications Inc., 2016) Kartal Yandım, Melis; Ceylan, Çağatay; Elmas, Efe; Baran, YusufChronic myeloid leukemia (CML) is a type of hematological malignancy that is characterized by the generation of Philadelphia chromosome encoding BCR/ABL oncoprotein. Tyrosine kinase inhibitors (TKIs), imatinib, nilotinib, and dasatinib, are used for the frontline therapy of CML. Development of resistance against these TKIs in the patients bearing T315I mutation is a major obstacle in CML therapy. Ponatinib, the third-generation TKI, is novel drug that is effective even in CML patients with T315I mutation. The exact mechanism of ponatinib in CML has been still unknown. In this study, we aimed to determine the potential mechanisms and structural metabolic changes activated by ponatinib treatment in imatinib-sensitive K562 human CML cell lines and 3 μM-imatinib-resistant K562/IMA3 CML cell lines generated at our lab. Apoptotic and antiproliferative effects of ponatinib on imatinib-sensitive and 3 μM-imatinib-resistant K562/IMA3 CML cells were determined by proliferation and apoptosis assays. Additionally, the effects of ponatinib on macromolecules and lipid profiles were also analyzed using Fourier transform infrared spectroscopy (FTIR). Our results revealed that ponatinib inhibited cell proliferation and induced apoptosis as determined by loss of mitochondrial membrane potential, increased caspase-3 enzyme activity, and transfer of phosphatidylserine to the plasma membrane in both K562 and K562/IMA-3 cells. Furthermore, cell cycle analyses revealed that ponatinib arrested K562 and K562/IMA-3 cells at G1 phase. Moreover, ponatinib treatment created a more ordered nucleic acid structure in the resistant cells. Although the lipid to protein ratio increased in imatinib-sensitive K562 cells with a little decrease in the K562/IMA-3 cells, ponatinib treatment indicated significant changes in the lipid composition such as a significant increase in the cellular cholesterol amounts much more in the K562/IMA-3 cells than the sensitive counterparts. Unsaturation in lipids was higher in the resistant cells; however, increases in lipids without phosphate and the number of acyl chains were much higher in the K562 cells. Taken together, all these results showed powerful antiproliferative and apoptotic effects of ponatinib in both imatinib-sensitive and imatinib-resistant CML cells in a dose-dependent manner, and hence, the use of ponatinib for the treatment of TKI-resistant CML patients may be an effective treatment approach in the clinic. More importantly, these results showed that FTIR spectroscopy can detect drug-induced physiological changes in cancer drug resistance.Article Citation - WoS: 73Citation - Scopus: 77Zinc Oxide and Zinc Hydroxide Formation Via Aqueous Precipitation: Effect of the Preparation Route and Lysozyme Addition(Elsevier Ltd., 2015) Top, Ayben; Çetinkaya, HayrullahAqueous precipitation products of Zn(NO3)2 and NaOH obtained by changing the method of combining the reactants and by using lysozyme as an additive were investigated. In the case of single addition method, octahedral ε-Zn(OH)2 and plate-like β-Zn(OH)2 structures formed in the absence and in the presence of lysozyme, respectively. Calcination of these Zn(OH)2 samples at 700 °C yielded porous ZnO structures by conserving the template crystals. When zinc source was added dropwise into NaOH solution, predominantly clover-like ZnO crystals were obtained independent of lysozyme addition. Mixed spherical and elongated ZnO morphology was observed when NaOH was added dropwise into Zn(NO3)2 solution containing lysozyme. Lysozyme contents of the precipitation products were estimated as in the range of ∼5-20% and FTIR indicated no significant conformational change of lysozyme in the composite. These results suggest that lysozyme-ZnO/Zn(OH)2 composite materials may have a value as an antibacterial material.Article Citation - WoS: 10Citation - Scopus: 10In-Situ Spectroscopic Ellipsometry and Structural Study of Hfo2 Thin Films Deposited by Radio Frequency Magnetron Sputtering(American Institute of Physics, 2014) Cantaş, Ayten; Özyüzer, Gülnur Aygün; Basa, Deepak KumarWe have investigated the reduction of unwanted interfacial SiO2 layer at HfO2/Si interface brought about by the deposition of thin Hf metal buffer layer on Si substrate prior to the deposition of HfO2 thin films for possible direct contact between HfO2 thin film and Si substrate, necessary for the future generation devices based on high-κ HfO2 gate dielectrics. Reactive rf magnetron sputtering system along with the attached in-situ spectroscopic ellipsometry (SE) was used to predeposit Hf metal buffer layer as well as to grow HfO2 thin films and also to undertake the in-situ characterization of the high-κ HfO2 thin films deposited on n-type 〈100〉 crystalline silicon substrate. The formation of the unwanted interfacial SiO2 layer and its reduction due to the predeposited Hf metal buffer layer as well as the depth profiling and also structure of HfO2 thin films were investigated by in-situ SE, Fourier Transform Infrared spectroscopy, and Grazing Incidence X-ray Diffraction. The study demonstrates that the predeposited Hf metal buffer layer has played a crucial role in eliminating the formation of unwanted interfacial layer and that the deposited high-κ HfO2 thin films are crystalline although they were deposited at room temperature.Article Citation - WoS: 55Citation - Scopus: 59Prediction of Various Chemical Parameters of Olive Oils With Fourier Transform Infrared Spectroscopy(Academic Press Inc., 2015) Uncu, Oğuz; Özen, BanuVibrational spectroscopic techniques offer advantages such as rapid and accurate measurements with minimum sample preparation and waste generation. In this study, it was aimed at determining some important quality parameters (oxidative stability, colour pigments, fatty acid profile and phenolic composition) of olive oils by Fourier transform infrared spectroscopy as one of the vibrational spectroscopic methods. Partial least square calibration models were constructed in order to reveal any correlation between quality parameters and spectral data. Regression coefficients for developed models showed that oxidative stability (0.99), chlorophyll content (0.98), some major fatty acids (palmitic (0.87), oleic (0.94), and linoleic acids (0.97), saturated (0.91), monounsaturated (0.94) and polyunsaturated fatty acids (0.97)), hydroxytyrosol as a phenolic compound (0.97) and total phenolic content (0.99) were predicted successfully. Variable influence on the projection values indicated that palmitic, vanillic and cinnamic acids and hydroxytyrosol are the most significant contributors to oxidative stability of olive oils. © 2015 Elsevier Ltd.Article Citation - WoS: 13Citation - Scopus: 13Macromolecular Changes in Nilotinib Resistant K562 Cells; an in Vitro Study by Fourier Transform Infrared Spectroscopy(SAGE Publications Inc., 2012) Ceylan, Çağatay; Camgöz, Aylin; Baran, YusufNilotinib is a second generation tyrosine kinase inhibitor which is used in both first and second line treatment of chronic myeloid leukemia (CML). In the present work, the effects of nilotinib resistance on K562 cells were investigated at the molecular level using Fourier transform infrared (FT-IR) spectroscopy. Human K562 CML cells were exposed to step-wise increasing concentrations of nilotinib, and sub-clones of K562 cells resistant to 50 nM nilotinib were generated and referred to as K562/NIL-50 cells. Antiproliferative effects of nilotinib were determined by XTT cell proliferation assay. Changes in macromolecules in parental and resistant cells were studied by FT-IR spectroscopy. Nilotinib resistance caused significant changes which indicated increases in the level of glycogen and membrane/lipid order. The amount of unsaturated lipids increased in the nilotinib resistant cells indicating lipid peroxidation. The total amount of lipids did not change significantly but the relative proportion of cholesterol and triglycerides altered considerably. Moreover, the transcriptional status decreased but metabolic turn-over increased as revealed by the FT-IR spectra. In addition, changes in the proteome and structural changes in both proteins and the nucleus were observed in the K562/NIL-50 cells. Protein secondary structural analyses revealed that alpha helix structure and random coil structure decreased, however, anti-parallel beta sheet structure, beta sheet structure and turns structure increased. These results indicate that the FT-IR technique provides a method for analyzing drug resistance related structural changes in leukemia and other cancer types.Article Kinetic and Structural Characterization of Interaction Between Trypsin and Equisetum Arvense Extract(Türk Biyokimya Derneği, 2014) Uslu, Mehmet Emin; Bayraktar, Oğuz; Ceylan, ÇağatayObjective: In this study the inhibitory effect of E. arvense extract on trypsin activity and the effect of trypsin on E. arvense extract were studied. In addition the nature of the interaction between the extract and trypsin was investigated. Methods: The inhibitory effect ethanol extract of E. arvense on trypsin activity was determined using trypsin enzyme assay. The structural effects of the extract-trypsin interaction for the extract were analyzed by FTIR. Finally, the HPLC analyses were carried out to analyze the individual components of the extract and the supernatant and soluble precipitate phases. Results: E. arvense extract was found to decrease total percent activity of trypsin to 5% in 24 hour at 24 °C. FTIR analyses indicated that the interaction between trypsin and E. arvense extract caused changes in the structure and hydrogen bonding behavior and composition of the extract proteins. These interactions also caused the extract lipids to accumulate in the insoluble precipitate phase. Most of the phenolics remained in the supernatant phase enhancing the inactivation of trypsin. However, the precipitated compounds were shown to be of apolar in nature as shown in the HPLC chromatograms. Conclusion: The methods that were used showed that the high phenolic content of E. arvense was the main reason for the inhibition of trypsin enzyme activity by denaturing the enzyme.Article Citation - WoS: 18Citation - Scopus: 20Impact of Incorporated Oxygen Quantity on Optical, Structural and Dielectric Properties of Reactive Magnetron Sputter Grown High-? Hfo2/Hf Thin Film(Elsevier Ltd., 2014) Cantaş, Ayten; Aygün, Gülnur; Turan, RaşitHigh-κ hafnium-oxide thin films have been fabricated by radio frequency (rf) reactive magnetron sputtering technique. To avoid formation of an undesired interfacial suboxide layer between Si and high-κ film, prior to HfO2 deposition, a thin Hf buffer layer was deposited on p-type (1 0 0) Si substrate at room temperature. Effect of oxygen gas quantity in the O2/Ar gas mixture was studied for the optical and structural properties of grown HfO2 high-κ thin films. The grown thin oxide films were characterized optically using spectroscopic ellipsometer (SE) in detail. Crystal structure was studied by grazing incidence X-ray diffractometer (GIXRD) technique, while bonding structure was obtained by Fourier transform infrared spectroscopy (FTIR) analyses. In agreement with GIXRD and FTIR analyses, SE results show that any increment above ideal quantity of oxygen content in the gas mixture resulted in decrements in the refractive index and thickness of HfO2 dielectric film, while increments in SiO2 thickness. It is apparent from experimental results that oxygen to argon gas ratio needs to be smaller than 0.2 for a good film quality. The superior structural and optical properties for grown oxide film were obtained for O2/Ar gas ratio of about 0.05-0.1 combined with ∼30 W constant rf sputtering power. © 2014 Elsevier B.V. All rights reserved.Article Citation - WoS: 4Citation - Scopus: 5Fourier Transform Infrared Spectroscopy as a Novel Approach for Analyzing the Biochemical Effects of Anionic Surfactants on a Surfactant-Degrading Arcobacter Butzleri Strain(SAGE Publications Inc., 2013) Sarıoğlu, Ömer Faruk; Tamer, Yusuf Talha; Özkan, Alper Devrim; Atabay, Halil İbrahim; Molva, Çelenk; Tekinay, TurgayAnionic surfactant-biodegrading capability of an Arcobacter butzleri strain was analyzed under aerobic conditions. The A. butzleri isolate displayed efficient surfactant-biodegrading capacity for sodium dodecyl sulfate (SDS) at concentrations of up to 100 mg/L in 6 days, corresponding to 99.0% removal efficiency. Fourier transform infrared spectroscopy was applied to observe the effects of varying concentrations of SDS on the biochemistry of bacterial cells. Results suggest that protein secondary structures were altered in bacterial cells at sufficiently high SDS concentrations, concurrent with SDS biodegradation.Article Citation - WoS: 16Citation - Scopus: 15The Roles of Macromolecules in Imatinib Resistance of Chronic Myeloid Leukemia Cells by Fourier Transform Infrared Spectroscopy(Elsevier Ltd., 2013) Baran, Yusuf; Ceylan, Çağatay; Camgöz, AylinImatinib is a first generation tyrosine kinase inhibitor, which is used for the treatment of chronic myeloid leukemia. However, resistance to imatinib is an important problem. Different mechanisms have been explained for imatinib resistance. In this study, we examined the roles of macromolecules in imatinib resistance in K562 cells at the molecular level using Fourier Transform Infrared (FT-IR) spectroscopy. An amount of 3μM imatinib resistant cells were generated by our group and named as K562/IMA-3 cells. Changes in macromolecules in parental and resistant cells were studied by FT-IR spectroscopy. Imatinib resistance caused changes, which indicated decreases in the level of glycogen and increases in the membrane order. The amount of unsaturated lipids increased in the imatinib resistant cells indicating lipid peroxidation. Imatinib resistance caused changes in the lipid/protein ratio. The relative protein content increased with respect to nucleic acids indicating higher transcription and protein expression and structural/organizational changes in the nucleus were evident as revealed by frequency changes in the nucleic acid bands. Changes in the amide bands revealed changes in the proteome of the resistant cells. Protein secondary structural changes indicated that the antiparallel beta sheet's structure increased, however the alpha helix structure, beta sheet structure, random coil structure and turns decreased in the resistant cells. These results indicate that the FT-IR technique provides a suitable method for analyzing drug resistance related structural changes in leukemia and other cancer types.