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Article Citation - WoS: 32Citation - Scopus: 32Urine 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, FilizUrine 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.Article Citation - WoS: 3Citation - Scopus: 4Nanoremediation 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, NurStenotrophomonas 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: 9Citation - Scopus: 9Ir-Spectroscopic Characterization of an Elongated Ompg Mutant(Elsevier Science inc, 2015) Korkmaz, Filiz; van Pee, Katharina; Yildiz, OezkanOmpG 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: 9Citation - Scopus: 9Urinalysis of Individuals With Renal Hyperfiltration Using Atr-Ftir Spectroscopy(Nature Portfolio, 2022) Kurultak, Ilhan; Sarigul, Neslihan; Kodal, Nil Su; Korkmaz, FilizAbnormal 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: 15Citation - Scopus: 13K+-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, WernerThe 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: 357Citation - Scopus: 374A New Artificial Urine Protocol To Better Imitate Human Urine(Nature Portfolio, 2019) Sarigul, Neslihan; Korkmaz, Filiz; Kurultak, IlhanArtificial 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: 2Citation - Scopus: 2Investigations of Ph-Dependent Dynamic Properties of Ompg-16sl, an Outer Membrane Protein G Mutant by Atr-Ftir Spectroscopy(Elsevier, 2022) Yilmaz, Irem; Korkmaz, FilizIn this paper, the dynamic properties of outer membrane protein G mutant (OmpG-16SL) are investigated with ATR-FTIR spectroscopy. While OmpG-WT has 14 beta-strands in its structure, the mutant is designed to have 16 beta-strands with the intention of creating an enlarged pore. Loop L6 is elongated by introducing six residues, two of which are negatively charged. The solvent accessibility of the OmpG-16SL mutant is compared with WT and a previously reported mutant OmpG-16S by tracking the H-1/H-2 exchange kinetics in acidic and neutral buffer conditions. The exchange kinetics and dynamics in the fast and slow exchange phases are separately investigated using the 2DCOS technique, which enables the tracking of the structural changes at each phase of the exchange process. The results suggest that the mutant OmpG-16SL is equally exposed to buffer in both acidic and neutral pH conditions. Additionally, the time range in the fast phase is very short - one-tenth of that for WT - and most of the exchange is completed in this phase. This fast exchange within minutes is also indicative of the presence of highly flexible and/or unstructured regions. In all, the fast exchange rates independent of the buffer pH justify the assumption that there is an altered interaction among the charged residues, which leads to a steadily-open pore. The role of the side-chain interactions within the pore and between the loops involving the loop L6 is also discussed.Article Structural and Electronic Properties of the Dppc Molecule(World Scientific Publ Co Pte Ltd, 2006) Erkoc, Sakir; Korkmaz, FilizThe 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.Article Citation - WoS: 2Citation - Scopus: 2Biosorption of Reactive Dyes by Novel Bacterium Leclercia Adecarboxylata: Complete Removal of Reactive Black 5 and Molecular Insights Into the Adsorption Mechanism(Wiley, 2025) Sen, Seda; Korkmaz, Filiz; Kilic, Nur KocberberLeclercia adecarboxylata isolated from the D & uuml;den Waterfall (Turkey) was utilized as a biosorbent for the removal of Reactive Black 5 (RB5), Setazol Blue BRF-X (BRF-X), Setazol Navy Blue SBG (SNB), and Setazol Turquoise Blue G (STBG). Of the dyes, RB5 was removed with the highest efficiency, 97.4% after 60 min. The effect of parameters such as pH (3-9), initial biosorbent dose (0.1-2.0 g/L), and initial dye concentration (25-1200 mg/L) on the biosorption of RB5 was investigated. Increasing the biosorbent dosage from 0.1 to 2.0 g/L enhanced the RB5 removal from 55.3% to 100% within 10 min. The complete removal (100%) of RB5 was achieved in media with 2.0 g/L biosorbent and 25 mg/L RB5 at pH 3 after 10 min. Additionally, the soluble extracellular polymeric substances (EPS) of L. adecarboxylata were found to consist of proteins, lipids, nucleic acids, and polysaccharides according to Fourier transform infrared spectroscopy (FTIR) analysis. The EPS was found to play a crucial role in dye removal, forming chemical interactions with dye molecules. Zeta potential analysis was used to evaluate the charge distribution on the biosorbent surface (-12.6 +/- 1.1 mV) and its interactions in the biosorption process. Kinetic and isotherm models suggested a complex interaction mechanism between the biomass and the dye. Adsorption isotherm data were analyzed via nine isotherm models. Among them, the Hill model was found to be the best fit for describing the equilibrium adsorption process of the RB5 (R2 = 0.9993). Overall, the applied models elucidated the influence of both physical and chemical interactions on the mechanism. Kinetic studies revealed that the adsorption of RB5 fit a pseudo-second-order kinetic model. The unique biochemical composition of the indigenous L. adecarboxylata biosorbent provided a high affinity for RB5, offering a sustainable, rapid, and economical solution for the treatment of dye-polluted water.Article Author Correction: Using Urine Ftir Spectra To Screen Autism Spectrum Disorder(Nature Portfolio, 2024) Sarigul, Neslihan; Bozatli, Leyla; Kurultak, Ilhan; Korkmaz, Filiz[No Abstract Available]
