Korkmaz Özkan, Filiz
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Korkmaz Ozkan,Filiz
K.,Filiz
F.,Korkmaz Ozkan
Filiz, Korkmaz Özkan
Korkmaz Ozkan,F.
K.Ö.Filiz
Korkmaz Özkan,F.
K. O. Filiz
Korkmaz F.
F.,Korkmaz Özkan
F., Korkmaz Ozkan
Filiz, Korkmaz Ozkan
Filiz Korkmaz Özkan
F., Korkmaz Özkan
Korkmaz Ozkan, Filiz
Korkmaz Özkan, Filiz
K. Ö. Filiz
K., Filiz
Özkan, Filiz Korkmaz
Korkmaz, Filiz
K.,Filiz
F.,Korkmaz Ozkan
Filiz, Korkmaz Özkan
Korkmaz Ozkan,F.
K.Ö.Filiz
Korkmaz Özkan,F.
K. O. Filiz
Korkmaz F.
F.,Korkmaz Özkan
F., Korkmaz Ozkan
Filiz, Korkmaz Ozkan
Filiz Korkmaz Özkan
F., Korkmaz Özkan
Korkmaz Ozkan, Filiz
Korkmaz Özkan, Filiz
K. Ö. Filiz
K., Filiz
Özkan, Filiz Korkmaz
Korkmaz, Filiz
Job Title
Profesör Doktor
Email Address
filiz.korkmaz@atilim.edu.tr
Main Affiliation
Physics Group
Status
Website
ORCID ID
Scopus Author ID
Turkish CoHE Profile ID
Google Scholar ID
WoS Researcher ID
Scholarly Output
19
Articles
17
Citation Count
391
Supervised Theses
1
19 results
Scholarly Output Search Results
Now showing 1 - 10 of 19
Article Citation - WoS: 0Citation - Scopus: 0Structural and Electronic Properties of the Dppc Molecule(World Scientific Publ Co Pte Ltd, 2006) Erkoc, Sakir; Korkmaz, Filiz; Physics GroupThe structural and electronic properties of the DPPC molecule have been investigated theoretically by performing semi-empirical self-consistent-field molecular-orbital theory calculations at the PM3 level in its ground state.Master Thesis İnsan İdrarları Arasında Gözlenen Çeşitliliğin Yapay İdrar Sistemi ve Ftır Spektroskopisi Kullanılarak Anlaşılması(2023) Ahmed, Marıam Hany Farouk Mohamed; Özkan, Filiz Korkmaz; Physics Groupİdrar testleri, çeşitli tıbbi bozuklukları tanımlamanın ve teşhis etmenin yaygın ve uygun bir yoludur. Bu çalışmada, 9 yapay idrar bileşeninin normal minimum ve maksimum değerlerinin spektrumunu belirlemek için yeni bir yapay idrar protokolünü (MP-AU) kullanıyoruz. Fourier Transform Infrared (FTIR) spektroskopisi, varsa bozuklukların erken saptanmasına yardımcı olacak bu spektrumları oluşturmak için kullanılmıştır. Hastanın idrar numunesinden elde edilen spektrum, minimum ve maksimum normal değerler için yapay idrar çözeltilerinden elde edilen spektrumlarla karşılaştırılabilir. Bu karşılaştırmanın sonucu hastanın sağlığı ile ilgili olacaktır. Hastanın spektrumu bu iki normal spektrum arasında yer alıyorsa, hastanın sağlık olduğu düşünülebilir. Buna bağlı olarak, hastanın spektrumu normal aralığın dışına çıkarsa, anomaliyi saptamak için daha fazla test istenebilir. Bu çalışmanın bulguları, yapay idrar sistemi içindeki bileşenlerin miktarının, FTIR spektrumundaki tepe noktalarının genlikleri ile ilişkili olduğunu ortaya koymaktadır. Ayrıca, daha sonraki çalışmalarda referans olarak kullanılmak üzere, test edilen idrar bileşenlerinin karakteristik bant pozisyonları da belirlenmiştir. Bu çalışma Atılım Üniversitesi Araştırma Destek programı çerçevesinde ATÜ-ADP-2122-01 numaralı proje ile finansal olarak desteklenmiştir.Article Citation - WoS: 1Citation - Scopus: 1Nanoremediation of Toxic Dyes Using a Bacterial Consortium Immobilized on Cellulose Acetate Nanofiber Mats(Wiley, 2024) Erkoc, Esra; Tuzun, Imre; Korkmaz, Filiz; San Keskin, Nalan Oya; Kocberber Kilic, Nur; Physics GroupStenotrophomonas maltophilia and Ochrobactrum sp. demonstrated the highest rates of dye bioremediation. The trials were performed at pH 8, which resulted in the highest bioremediation rate of 64.6% in media containing 21.2 mg L-1 dye. As the dye concentration increased, the pollutant removal decreased, with the maximum bioremoval rate of 70.3%. The removal capacity was increased with an increase in biomass concentration; the highest yield of 91.3% was obtained in media containing 14.2 mg L-1 dye and 12% (v/v) biomass. In nanoremediation studies, the bacterial consortium was immobilized on cellulose acetate nanofiber mats (CA-NFM). Scanning electron microscopic micrographs showed that bead-free nanofiber mats were effective in immobilizing bacterial cells. Moreover, nanofiber structures were capable of supporting exopolysaccharides formation, as confirmed by Fourier transform & imath;nfrared spectroscopy. The bacterial consortium immobilized on CA-NFM showed a maximum bioremoval rate of 56.5%. Reusability tests demonstrated that the consortium immobilized CA-NFM could be used at least five times. Furthermore, after leaving the mat for 1 month at 4 degrees C, it was still usable, and the removal efficiency was found to be 45.4%. Based on our findings, bacteria immobilized on CA-NFM have the potential to be used as highly effective and versatile nanobiotechnological biological sorbents in the treatment of wastewater containing dyes.Article Citation - WoS: 8Citation - Scopus: 8Ir-Spectroscopic Characterization of an Elongated Ompg Mutant(Elsevier Science inc, 2015) Korkmaz, Filiz; van Pee, Katharina; Yildiz, Oezkan; Physics GroupOmpG is a nonselective, pH dependent outer membrane protein from Escherichia coli. It consists of 281 residues, forming a 14-stranded beta-sheet structure. In this study, OmpG is extended by 38 amino acids to produce a 16-stranded beta-barrel (OmpG-16S). The resulting protein is investigated by IR-spectroscopy. The secondary structure, pH-dependent opening/closing mechanism, buffer accessibility and thermal stability of OmpG-16S are compared to OmpG-WT. The results show that OmpG-16S is responsive to pH change as indicated by the Amide I band shift upon a switch from acidic to neutral pH. This spectral shift is consistent with that observed in OmpG-WT, which confirms the existence of structural differences consistent with the presence of the open or closed state. Secondary structure analysis after curve-fitting of Amide I band revealed that the additional residues do not fold into beta-sheet; rather they are in the form of turns and unordered structure. In thermal stability experiments, OmpG-16S is found to be as stable as OmpG-WT. Additionally, H/D exchange experiments showed no difference in the exchange rate of OmpG-16S between the acidic and alkaline pH, suggesting that the loop L6 is no longer sufficient to block the pore entrance at acidic pH. (C) 2015 Elsevier Inc. All rights reserved.Article Citation - WoS: 89Citation - Scopus: 93Effect of Progesterone on Dppc Membrane: Evidence for Lateral Phase Separation and Inverse Action in Lipid Dynamics(Elsevier Science inc, 2005) Korkmaz, F; Severcan, F; Physics GroupInteractions of progesterone with zwitterionic dipalmitoyl phosphatidylcholine (DPPC) triultilamellar liposomes were investigated as a function of temperature and progesterone concentration by using three non-invasive techniques namely Fourier transform infrared spectroscopy, turbidity at 440 nm, and differential scanning calorimetry. The results reveal that progesterone changes the physical properties of DPPC bilayers by decreasing the main phase-transition temperature, abolishing the pre-transition, broadening the phase-transition profile, disordering the system both in gel and liquid crystalline phase, increasing the dynamics at low concentrations whereas stabilizing the membrane at high concentrations, and inducing phase separation. Progesterone does not change the hydration of the C=O groups, while it strengthens the hydrogen bonding between the PO (2) over bar groups of lipids and the water molecules around. (c) 2005 Elsevier Inc. All rights reserved.Article Citation - WoS: 5Citation - Scopus: 5Concentration Dependent Different Action of Progesterone on the Order, Dynamics and Hydration States of the Head Group of Dipalmitoyl-Phosphatidylcholine Membrane(Hindawi Ltd, 2005) Korkmaz, F; Kirbiyik, H; Severcan, F; Physics GroupInteractions of progesterone with zwitterionic dipalmitoyl phosphatidylcholine (DPPC) multilamellar liposomes (MLVs) were investigated as a function of progesterone concentration at selected temperatures monitoring both the gel and liquid crystalline phase, by using Fourier Transform Infrared spectroscopy (FTIR). It has been show that the effect of progesterone on membrane dynamics is dependent on progesterone concentration. At 1 mol%, which is close to physiological level, progesterone behaves differently. At this concentration the decrease in dynamics is more noticeable. Additionally a dramatic decrease in the strength of hydrogen bonding in the interfacial region of the bilayer is also observed. When concentration increases up to 12 mol% opposite behaviour is observed at all interactions. Above 12 mol%, progesterone-DPPC interactions shows almost linear plot.Article Citation - WoS: 14Citation - Scopus: 12K+-induced Conformational Changes in the Trimeric Betaine Transporter Betp Monitored by Atr-Ftir Spectroscopy(Elsevier Science Bv, 2013) Korkmaz, Filiz; Ressl, Susanne; Ziegler, Christine; Maentele, Werner; Physics GroupThe trimeric Na+-coupled betaine symporter BetP from Corynebactrium glutamicum adjusts transport activity according to the external osmolality. BetP senses the increasing internal K+ concentration, which is an immediate consequence of osmotic upshift in C. glutamicum. It is assumed that BetP specifically binds potassium to yet unidentified binding sites, thereby inducing conformational changes resulting in activation. Atomic structures of BetP were obtained in the absence of potassium allowing only a speculative glimpse on a putative mechanism of K+-induced transport activation. The structural data suggest that activation in BetP is crucially linked to its trimeric state involving an interaction network between several arginines and glutamates and aspartates. Here, we describe the effect of K+-induced activation on the specific ionic interaction sites in terminal domains and loops and on the protomer-protomer interactions within the trimer studied by ATR-FTIR spectroscopy. We suggest that arginine and aspartate and/or glutamate residues at the trimeric interface rearrange upon K+-induced activation, although they remain assembled in an interaction network. Our data propose a two-step mechanism comprising first a change in solvent exposure of charged residues and second a modification of their interaction sites in a partner-switching manner. FTIR reveals a higher alpha-helical content than expected from the X-ray structures that we attribute to the structurally unresolved N-terminal domain modulating regulation. In situ H-1/H-2 exchange studies point toward an altered exposure of backbone regions to buffer solution upon activation, most likely due to conformational changes in both terminal domains, which further affects ionic interactions within the trimer. (C) 2013 Elsevier B.V. All rights reserved.Article Citation - WoS: 2Citation - Scopus: 5Urinalysis of Individuals With Renal Hyperfiltration Using Atr-Ftir Spectroscopy(Nature Portfolio, 2022) Kurultak, Ilhan; Sarigul, Neslihan; Kodal, Nil Su; Korkmaz, Filiz; Physics GroupAbnormal increased glomerular filtration rate (GFR), otherwise known as renal hyperfiltration (RHf), is associated with an increased risk of chronic kidney disease and cardiovascular mortality. Although it is not considered as a disease alone in medicine today, early detection of RHf is essential to reducing risk in a timely manner. However, detecting RHf is a challenge since it does not have a practical biochemical marker that can be followed or quantified. In this study, we tested the ability of ATR-FTIR spectroscopy to distinguish 17 individuals with RHf (hyperfiltraters; RHf (+)), from 20 who have normal GFR (normofiltraters; RHf(-)), using urine samples. Spectra collected from hyperfiltraters were significantly different from the control group at positions 1621, 1390, 1346, 933 and 783/cm. Intensity changes at these positions could be followed directly from the absorbance spectra without the need for pre-processing. They were tentatively attributed to urea, citrate, creatinine, phosphate groups, and uric acid, respectively. Using principal component analysis (PCA), major peaks of the second derivative forms for the classification of two groups were determined. Peaks at 1540, 1492, 1390, 1200, 1000 and 840/cm were significantly different between the two groups. Statistical analysis showed that the spectra of normofiltraters are similar; however, those of hyperfiltraters show diversity at multiple positions that can be observed both from the absorbance spectra and the second derivative profiles. This observation implies that RHf can simultaneously affect the excretion of many substances, and that a spectroscopic analysis of urine can be used as a rapid and non-invasive pre-screening tool.Article Citation - WoS: 268Citation - Scopus: 273A New Artificial Urine Protocol To Better Imitate Human Urine(Nature Portfolio, 2019) Sarigul, Neslihan; Korkmaz, Filiz; Kurultak, Ilhan; Physics GroupArtificial urine has many advantages over human urine for research and educational purposes. By closely mimicking healthy individuals' urine, it may also be important in discovering novel biomarkers. However, up until now, there has not been any specific protocol to prove the similarity in terms of the chemical composition at the molecular level. In this study, a new artificial urine protocol is established to mimics the urine of healthy individuals. The multi-purpose artificial urine (MP-AU) presented here is compared with two other protocols most cited in literature. Furthermore, these three protocols are also compared with samples from 28 healthy young individuals. To do so, attenuated total reflection-Fourier transform infrared spectroscopy (ATR-FTIR) is used, according to which MP-AU shows a significantly close similarity with human urine. In formulating MP-AU, the infrared spectra of nine compounds is provided, making possible the band assignment of some absorption bands to certain compounds. Given its properties, the MP-AU protocol introduced here is both economical and practical, making it useful when designing comparative-controlled experiments.Article Citation - WoS: 22Citation - Scopus: 21Urine Analysis Using Ftir Spectroscopy: a Study on Healthy Adults and Children(Wiley-v C H verlag Gmbh, 2021) Sarigul, Neslihan; Kurultak, Ilhan; Gokceoglu, Arife Uslu; Korkmaz, Filiz; Physics GroupUrine spectra from 108 healthy volunteers are studied by attenuated total refraction-Fourier transform infrared (ATR-FTIR) spectroscopy. The spectral features are correlated with observable urine components. The variation of spectra within a healthy population is quantified and a library of reference spectra is constructed. Using the band assignments, these spectra are compared with both age-wise and gender-wise. Children show the least intensity variations compared to both adult groups. Young adults show the highest variation, particularly in the 1650 to 1400 cm(-1) and 1200 to 900 cm(-1) regions. These results indicate the importance of the size of the control group in comparative studies utilizing FTIR. Age-wise comparisons reveal that phosphate and sulfate excretion decreases with age, and that the variance of phosphate among individuals is higher with adults. As for gender-wise comparisons, females show a slightly higher citrate content at 1390 cm(-1) regardless of the age and they show a higher variance in the 1200 to 1000 cm(-1) region when compared to men.
