Scopus İndeksli Yayınlar Koleksiyonu / Scopus Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/11147/7148
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Article Citation - WoS: 2Citation - Scopus: 2A Novel Approach Utilizing Rapid Thin-Film Microextraction Method for Salivary Metabolomics Studies in Lung Cancer Diagnosis(Elsevier, 2024) Pelit, Fusun; Erbas, Ilknur; Ozupek, Nazli Mert; Gul, Merve; Sakrak, Esra; Ocakoglu, Kasim; Goksel, Ozlem; Özdemir, DurmuşThis study investigated the potential of targeted salivary metabolomics as a convenient diagnostic tool for lung cancer (LC), utilizing a rapid TFME-based method. It specifically examines TFME blades modified with SiO2 nanoparticles, which were produced using a custom-made coating system. Validation of the metabolite biomarker analysis was performed by these blades using liquid chromatography-tandem mass spectroscopy (LCMS/MS). The extraction efficiencies of SiO2 nanoparticle/polyacrylonitrile (PAN) composite-coated blades were compared for 18 metabolites. Response surface methodology (RSM) was used to optimize the analysis conditions. Linear calibration plots were obtained for all metabolites at concentrations between 0.025 to 4.0 mu g/mL in the presence of internal standard, with correlation coefficients (R-2) ranging from 0.9975 to 0.9841. The limit of detection (LOD) and limit of quantitation (LOQ) were in the range of 0.014 to 0.97 mu g mL(-1) and 0.046 to 3.20 mu gmL(-1), respectively. The %RSD values for all analytes were within the acceptable range (less than 20 %) for the proposed method. The method was applied to the saliva samples of 40 patients with LC and 38 healthy controls. The efficacy of metabolites for LC diagnosis was determined by in silico methods and the results reveal that phenylalanine and purine metabolism metabolites (e.g., hypoxanthine) are of great importance for LC diagnosis. Furthermore, potentially significant biomarker analysis results from the ROC curve data reveal that proline, hypoxanthine, and phenylalanine were identified as potential biomarkers for LC diagnosis.Article Citation - WoS: 3Citation - Scopus: 41,2-Diboranes With Strong Donor Substitutes: Synthesis, Ovicidal and Larvicidal Effect on Important Vector Species(Elsevier, 2024) Bursali, Fatma; Sahin, Yueksel; Aygun, Muhittin; Sevincek, Resul; Biyik, H. Halil; Özgener, Hüseyin; Gurbuz, BurcinNovel control products are needed in the control of important insects like mosquitoes which are developing resistance to insecticides and larvicides currently in the market. Boron compounds have been demonstrated to exhibit antibacterial and anticancer effects. 1,2-diboranes with a long history and importance in boron chemistry have been described. These compounds are synthesized from reactions of 1,2-dichlordiborane derivatives with lidium amides (ArNHLi/Et2NLi, etc.). In addition to the three previously synthesized diborane compounds, five novel 1,2-diborane compounds were synthesized in good yield using the same method for the first time. The structures of the novel derivatives were characterized by nuclear magnetic resonance spectroscopy, and the molecular structure of one of them (2a) was also demonstrated using single crystal X-ray diffraction. In this preliminary study, the ovicidal and larvicidal effects of new 1,2-diamino-1,2-diborane derivatives against Aedes aegypti and Aedes albopictus eggs and larvae were investigated for the first time. Of these, 2a and 2e showed the highest ovicidal activity against both species, while 7, 4 and 2d showed particularly high larvicidal activity. Some 1,2-diborane derivatives were found to be significantly toxic, with LC50 values ranging from 14,930 to 27,975 mu g/mL. Some derivatives (6, 2a, 2c) were less effective against mosquito larvae. 1,2-Diborane derivatives have high ovicidal and larvicidal effects on mosquitoes and are therefore potential candidates for the development of new larvicides. Further studies are needed to evaluate its mode of action and safety. Understanding their mode of action against mosquito development is crucial to optimizing their use and reducing the potential development of resistance. Their potential effects on other mosquito species and non -target organisms need to be investigated.Article Citation - Scopus: 3Development of Chrono-Spectral Gold Nanoparticle Growth Based Plasmonic Biosensor Platform(Elsevier, 2024) Sözmen, Alper Baran; Elveren, Beste; Erdoğan, Duygu; Mezgil, Bahadır; Baştanlar, Yalın; Yıldız, Ümit Hakan; Arslan Yıldız, AhuPlasmonic sensor platforms are designed for rapid, label-free, and real-time detection and they excel as the next generation biosensors. However, current methods such as Surface Plasmon Resonance require expertise and well-equipped laboratory facilities. Simpler methods such as Localized Surface Plasmon Resonance (LSPR) overcome those limitations, though they lack sensitivity. Hence, sensitivity enhancement plays a crucial role in the future of plasmonic sensor platforms. Herein, a refractive index (RI) sensitivity enhancement methodology is reported utilizing growth of gold nanoparticles (GNPs) on solid support and it is backed up with artificial neural network (ANN) analysis. Sensor platform fabrication was initiated with GNP immobilization onto solid support; immobilized GNPs were then used as seeds for chrono-spectral growth, which was carried out using NH2OH at varied incubation times. The response to RI change of the platform was investigated with varied concentrations of sucrose and ethanol. The detection of bacteria E.coli BL21 was carried out for validation as a model microorganism and results showed that detection was possible at 102 CFU/ml. The data acquired by spectrophotometric measurements were analyzed by ANN and bacteria classification with percentage error rates near 0% was achieved. The proposed LSPR-based, label-free sensor application proved that the developed methodology promises utile sensitivity enhancement potential for similar sensor platforms. © 2024 The Author(s)Article Citation - WoS: 6Citation - Scopus: 6A Novel 2-Aminophenalenone Fluorescent Probe Designed for Monitoring H2o2 for in Vitro and in Vivo Bioimaging(Elsevier, 2024) Saygılı, Ecem; Ersöz Gülseven, Esra; Kıbrıs, Erman; Çakan Akdoğan, Gülçin; Üçüncü, MuhammedA significant compound in living organisms, hydrogen peroxide (H2O2) plays a dual role as a signalling molecule in cellular communication and as a pivotal biomarker in assessing disease and oxidative stress. Thus, the detection of abnormal changes in H2O2 levels is essential to understanding its function and involvement in biological systems. The growing demand to meet the specific needs for applications, particularly in biological systems, has sharpened focus on highly sensitive, highly selective molecular sensors and, in turn, heightened interest in these diagnostic tools with innovative designs. In our study, 2-aminophenalenone (2-AP) was used for the first time as a fluorophore in a fluorescent probe. The 2-APB molecule obtained from the reaction of 2-AP with 4-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl) benzyl chloroformate exhibited a highly selective and sensitive (i.e. 62 nM) detection profile for H2O2 compared with the other reactive oxygen species, anions, and metal cations. Moreover, offering naked-eye detection in aqueous solutions, 2-APB demonstrated excellent sensing performance, detection and real-time monitoring in relation to exogenous H2O2 in cells and endogenous H2O2 in zebrafish embryos. © 2024 Elsevier B.V.Article Citation - WoS: 2Citation - Scopus: 3A Phenomenological Kinetic Flotation Model: Distinct Time-Variant Floatability Distributions for the Pulp and Froth Materials(Elsevier, 2023) Polat, Mehmet; Polat, HürriyetA simple and easy-to-use phenomenological kinetic flotation model, strongly connected with the physics of the process, is proposed in this paper. The model explicitly contains the cell volume, aeration rate, volumetric holdup, mean bubble size, and particle density as input variables. It can be employed to characterize the floatability distributions of the particles in the pulp and the froth separately any time during the flotation process. Two new time-dependent kinetic parameters, the bubble loading factor & phi;(t) and the maximum cell mass transfer capacity Mmax(t) also appear in the model expression. & phi;(t) is a measure of the degree of crowding of the bubble surfaces and accounts for the deviations from the first-order rate equation. Mmax(t) describes the maximum amount of mass that can be transported to the froth phase by the bubble population in the cell. Screen fractionation of each froth product collected at different time intervals during a single kinetic flotation test is sufficient to generate the data required by the model for analysis. Application of the model to this data yields directly time-dependent functions for the floatability of the particles reporting to froth Kf(t) or remaining in the cell Kp(t) for each size fraction separately, without the need for any empirical parameters. The test of the model was carried out using published kinetic flotation data from the literature.Article Citation - WoS: 5Citation - Scopus: 4Polarity Induced Vapochromism and Vapoluminescence of Polythiophene Derivatives for Volatile Organic Compounds Classification(Elsevier, 2023) Karabacak, Soner; Qun, David Lee Chao; Ammanath, Gopal; Yeasmin, Sanjida; Yağmurcukardeş, Mehmet; Palaniappan, Alagappan; Liedberg, Bo; Yıldız, Ümit HakanPolarity induced vapochromic and vapoluminescent properties of cationic poly-3-alkoxythiophene derivatives (PT) casted on polyvinylidene fluoride (PVDF) membranes are reported. PT with six different pendant groups are designed to differentially interact with volatile organic compounds (VOC) of varying polarities, thereby enabling their classification. PT exhibit a rapid vapochromic response with a concurrent modulation of vapoluminescence due to the non-covalent cation-? interactions between the pendant groups and the PT backbone. Adsorption of VOC on pendant groups alters the conformation of PT backbone, thus resulting in an increase in intensity and blue shifting of fluorescence emission within the visible spectrum. The vapoluminescent responses are found to be more sensitive with a limit of detection (LOD) of ?7 ppm and a wider dynamic range as compared to the vapochromic responses with a LOD of ?60 ppm for the detection of a model VOC: chloroform. Notably, all the PT illustrate an instantaneous recovery of colour and luminescence upon desorption of VOC. PT interaction with VOC of varying polarities was ascertained using density functional theory (DFT) and principal component analysis (PCA) methodologies. In summary, the polarity induced vapochromic and vapoluminescent properties of PT could yield a selective and sensitive vapochromic and fluorometric dual-mode VOC detection platform. © 2023Article Citation - WoS: 9Citation - Scopus: 8Quantitative Determination of Phenolic Compounds in Propolis Samples From the Black Sea Region (türkiye) Based on Hptlc Images Using Partial Least Squares and Genetic Inverse Least Squares Methods(Elsevier, 2023) Güzelmeriç, Etil; Özdemir, Durmuş; Şen, Nisa Beril; Çelik, Cansel; Yeşilada, ErdemThe complex chemical composition of propolis is related to the plant source to be used by honeybees. Propolis type is defined based on the plant source with the highest proportion in its composition, which is determined by chromatographic techniques as high-performance thin-layer chromatography (HPTLC). In addition to marker component identification to specify the propolis type, quantification of its proportion is also significant for prediction and reproducible pharmacological activity. One drawback for propolis marker component quantita-tion is that during the chromatographical analysis, not the main but the other plant sources with less proportion may cause interferences during the chemical analysis. In this study, the amounts of marker components were compared with the reference analysis data obtained by high-performance liquid chromatography (HPLC) and from HPTLC images using Partial Least Squares (PLS) and Genetic Inverse Least Squares (GILS) regression methods. Firstly, HPTLC images of propolis samples were processed by an image algorithm (developed in MATLAB) where the bands of each standard and the samples were cut same dimensional pieces as 351 x 26 pixels in height and width, respectively. Simultaneously, reference analysis of the marker components in propolis samples was performed with a validated HPLC method. Consequently, the reference values obtained from HPLC versus PLS, and GILS predicted values of the eight compounds based on the digitized HPTLC images of the chromatograms were found to be matched successfully. The results of the multivariate calibration models demonstrated that HPTLC images could be used quantitatively for quality control of propolis used as a food supplement.Article Citation - WoS: 15Citation - Scopus: 15Sorafenib Loaded Zif-8 Metal-Organic Frameworks as a Multifunctional Nano-Carrier Offers Effective Hepatocellular Carcinoma Therapy(Elsevier, 2023) Mete, Derya; Yemeztaşlıca Yetişkin, Egehan; Şanlı Mohamed, GülşahHepatocellular carcinoma (HCC) is a primary malignant neoplasia of the liver and sorafenib is one of the most commonly used drugs in the treatment of HCC. Due to undesirable nature and side effects of sorafenib, nano-drug delivery systems are being developed. A member of metal-organic frameworks (MOFs), ZIF-8 offers a very suitable platform for drug transport and controlled drug release due to its zinc content and pH-sensitive, biodegradable in an acidic environment. In the present study, sorafenib was encapsulated in ZIF-8 material with 53.8% efficiency and 58% loading capacity (SRF@ZIF-8). Structural characterizations of synthesized ZIF-8 and SRF@ZIF-8 system were investigated in details. Drug release analysis exhibited a faster release profile at pH 5.0 compared to that of pH 7.4. The cytotoxic effects of sorafenib and zinc were investigated in HepG2 and HuH-7 cell lines in vitro. The results demonstrated that in addition to sorafenib, ZIF-8 provided zinc to the envi-ronment with its biodegradable structure resulted in an effective cytotoxic effect on HCC cells. The findings showed that a formulation combining zinc and sorafenib together was more effective in HCC treatment compared to sorafenib itself.Article Molecular Dynamics Simulation of Ssdna and Cationic Polythiophene(Elsevier, 2023) Nalıncı Bardak, Nehir; Kıbrıs, Erman; Demirci, Fethi Can; Elmacı Irmak, NuranIn this work, molecular dynamics simulations of complexes composed of single strand DNA (ssDNA) sequences and cationic oligothiophenes are performed to understand experimental findings and the sensing ability of polythiophene electrolytes toward ssDNA. The simulation results exhibit no significant structural effect for replacing the cationic amine moiety with imidazole derivative on the side group of the oligomer. Adding a homopurine strand elongates the oligomer backbone; on the contrary, mixing up the homopyrimidine strand causes compression. On the other hand, these ssDNAs do not notably affect the compactness of the oligomer backbones. The anion-cation interactions play an essential role in the structural and spectroscopic change of cationic polythiophenes (CPTs) upon complexation with ssDNAs. The red shift of CPTs in the UV-VIS spectra with the addition of homopurine strands might be explained by the strong anion-cation, weak pi -cation interactions, and high binding affinities. Nonpolar interactions (vdW and SA) and complex solvation energies dominate binding free energies. Hydrogen interaction analyses show that oligomers most likely approach the ssDNAs from their backbone upon complexation except for the duplex containing homopyrimidine strand and oligothiophene possessing imidazole derivative side chain.Article Citation - WoS: 3Citation - Scopus: 3Synthesis and Antifungal and Antibacterial Bioactivities of Diborolanes Containing Arylamines(Elsevier, 2023) Aygün, Muhittin; Sevinçek, Resul; Özgener, Hüseyin; Bıyık, Hacı Halil; Metin, Kubilay; Şahin, Yüksel; Poyrazoğlu Çoban, Esra; Gürbüz, BurçinA good yield of 1,2-diarylamino-1,2-diborolanes 2 was obtained from the reaction of 1,2-dichloro-1,2-diborolane 1 and ArNHLi (an anilide). The structures of these new derivatives were characterized by nuclear magnetic resonance spectroscopy. The molecular structures of 2a and 2b were also determined using single-crystal X-ray diffraction. Antimicrobial activities of synthesized compounds against some Gram-positive and -negative bacteria and yeasts were determined. Some compounds were found to have strong antibacterial and antifungal properties, especially against the bacterium, S. pneumonia, which is the causative agent of pneumonia, and the fungus, C. albicans, which is the causative agent of candidiasis. The compounds 2a and 3 had a powerful effect (compound 2a and 3 = 1 μgmL−1) against S. pneumoniae ATCC 27336 bacteria. In addition, compounds 2a, 3 and 2f were observed to have strong effects (compound 2a, 3, 2f = 2 μgmL−1) against C. albicans ATCC 10231 and C. utilis ATCC 9950. The results obtained were found to be more effective than the MIC values (128–64 μgmL−1) of Streptomycin and Flukanozol drugs used for bacteria and yeasts. The results of our study show that the synthesized substances can be used for new drug applications that are being developed against infectious diseases in the pharmaceutical industry. © 2023 Elsevier B.V.