Scopus İndeksli Yayınlar Koleksiyonu / Scopus Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/11147/7148
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Article Anticancer Properties of Newly Synthesized Pyrrole Derivatives as Potential Tyrosine Kinase Inhibitors(Wiley, 2026) Kaya, Meltem; Kara, Yunus; Sanli-Mohamed, GulsahThe anticancer activity of a series of newly synthesized pyrrole derivatives was systematically evaluated in HeLa cervical cancer cells, focusing on their potential as tyrosine kinase inhibitors and modulators of the mTOR signaling pathway. This study builds on our previous synthetic work by investigating the biological effects of seven structurally characterized compounds (d1-d7). Among them, compounds d1 and d3 exhibited the most potent cytotoxicity, with IC50 values of 140.6 mu M and 366.4 mu M, respectively, after 48 h of treatment. Both compounds significantly impaired cell cycle progression-d1 induced S-phase arrest, while d3 caused G1-phase arrest-and markedly suppressed cell migration in wound healing assays. Mechanistically, these effects were accompanied by reduced phosphorylation of p70S6K (Thr389, Ser421/424) and increased p-4EBP1, indicating inhibition of mTORC1 signaling. These findings suggest that d1 and d3 are promising lead compounds with dual antiproliferative and anti-migratory activity in cervical cancer, mediated through modulation of the PI3K/Akt/mTOR axis.Article Linking RNA Methylation to Structure: A Biophysical Perspective(Wiley, 2026) Akgul, Bunyamin; Guler, Gunnur; Saglam, Buket; Akkus, Onur; Akcaoz-Alasar, AzimeRecent epitranscriptomic studies show that ribonucleic acids (RNAs) are coated with an array of chemical modifications that dictate their cellular fate. Genetic, biochemical, and genomic approaches have been employed to elucidate the molecular details of RNA methylation, one of the most prevalent types of RNA modifications with significant implications for health and disease. Various biochemical approaches have been developed to identify RNA methylations both at the global and nucleotide resolution levels. However, simpler detection methods are needed to assess the global methylation status of synthetic or cellular RNAs. Although significant progress has been made in elucidating the factors involved in writing, erasing, or reading methylated epitopes or structures, the impact of these methyl moieties on the secondary structure of RNAs or macromolecular interactions remains to be fully understood. Typically, biophysical approaches, such as Fourier transformed-infrared (FT-IR) spectroscopy, circular dichroism (CD), and Raman spectroscopy, have been used to study the structures and interactions of macromolecules, including DNA and proteins. Although RNAs harbor similar chemical modifications or structure-mediated functions, the number of RNA studies that employ biophysical approaches is scarce. In this viewpoint article, we present a biophysical perspective that links RNA methylation to structure and propose that FT-IR analyses can be employed to examine global changes in the abundance of cellular RNA m(6)A marks. Additionally, we discuss the potential applications of biophysical approaches that may be employed to gain insight into methylation-mediated changes in RNA structures.Article Analytical Methodology for Monitoring and Distribution Pattern Analysis of Polycyclic Aromatic Hydrocarbons in River Basins Based on Chemometrics(Wiley, 2025) Yildirim, Ebru calkan; Pelit, Fusun; Ozdemir, Durmus; Kazan, Aysegul; Tasdelen, Ozge; Baycan, NevalWith the increase in urbanization and industrialization, the environmental quality of river basins, which serve as a crucial source of irrigation for agricultural activities, has been deteriorating progressively. Thus, monitoring persistent toxic substances in urban water resources is crucial for maintaining ecological stability and protecting human health. In recent years, particular attention has been directed toward the prevention of polyaromatic hydrocarbons (PAHs), highlighting the importance of analyzing these compounds in water samples through more environmentally sustainable techniques. In this study, we report a green, rapid, cost-effective and simple dispersive liquid-liquid extraction (DLLME) method to monitor PAHs in river waters taken from 21 stations located within the geographical boundaries of the Gediz River Basin in Izmir Province, T & uuml;rkiye. Methodological parameters were optimized by chemometric techniques including Plackett-Burman (PBD) and Box-Behnken design. The method's accuracy was tested upon spiked river samples, and the recoveries ranged from 80% to 102%. The calibration curves were linear, with correlation coefficients greater than 0.98. The limit of detection values were between 0.01 and 0.05 ng mL-1. The reproducibility (RSD%) varied from 4.0% to 19%. Multivariate classification methods such as principal component analysis (PCA) and hierarchical cluster analysis (HCA), along with the supervised classification method partial least squares discriminant analysis (PLS-DA) were applied to elucidate the general distribution patterns of individual PAHs in the basin water samples. The chemometric evaluation conducted across four seasons revealed that PAH contamination was higher in the fall and winter months, resulting in a clear separation from spring and summer samples by using the first two principal components.Article Citation - WoS: 1The Impact of Oxygen and Antimicrobial Tea Tree Oil Carrying Biomaterial on Cell Viability Under Hypoxic Conditions(Wiley, 2025) Demir, Yagmur Damla; Tepeli, Dilek; Guvensen, Mahmut Deniz; Soyer, Ferda; Akin, Ozlem; Kehr, Nermin SedaTraditional wound treatment involves protecting the wound with dressing and administering antibiotics to prevent tissue infection due to bacteria. However, these methods are inadequate due to the side effects of antibiotics on healthy cells and microbial resistance to antibiotics. Therefore, new strategies involving the application of natural resources such as essential oils as antimicrobial agents in combination with biomaterials as wound dressings have been tested in the treatment of wounds. Furthermore, oxygen (O2)-releasing biomaterials have attracted great interest due to the important role of O2 in wound healing processes. However, the co-application of O2 and essential oil as antimicrobial and cell-promoting agents has not been studied. In this context, we report a novel biomaterial capable of co-delivering O2 and natural antimicrobial tea tree oil (TTO) for 15 and 5 days, respectively. The biomaterial consists of an alginate scaffold (Alg-PMOF-O) containing O2-carrying nanomaterial, laponite and TTO. In vitro bacterial experiments have shown that O2 release from Alg-PMOF-O is an additional parameter acting as an antibacterial agent to inhibit bacterial growth but is not sufficient alone to inhibit bacteria. 5 mu L of TTO in Alg-PMOF-O is necessary to suppress both E. coli and S. aureus over a 1-day incubation period. The effect of TTO and O2 alone or in combination on cell viability is examined using WST-1 and PrestoBlue assays. According to the WST-1 and PrestoBlue tests, the combined application of TTO and O2 does not show any toxic effect on fibroblast cells under normoxic conditions during the 5-day incubation period. Under hypoxic conditions, the WST-1 test shows no toxic effect after only 1 day of incubation, while the PrestoBlue test shows no toxicity under hypoxia during both 1 and 5 days of incubation. On the other hand, the combined application of TTO and O2 indicates toxic effects on cancer Malme-3M cells during both normoxic and hypoxic conditions over 1 and 5 days of incubation. This effect is confirmed by both the WST-1 and PrestoBlue tests. The overall results demonstrate that Alg-PMOF-O exhibits antibacterial activity while having a lower toxic effect on fibroblasts under hypoxic conditions, and therefore has potential for use as wound dressing.Article Citation - WoS: 1Toxicological Assessment of Melamine-Functionalized Graphene Oxide and Carbon Nanotubes Using Zebrafish Models(Wiley, 2025) Yigit, Aybek; Yildirim, Serkan; Kokturk, Mine; Nazli, Dilek; Kiliclioglu, Metin; Ozhan, Gunes; Menges, NurettinGraphene oxide (GO) and carbon nanotube (CNT)-based nanomaterials have attracted significant interest in various industrial and biomedical applications due to their unique physicochemical properties; however, concerns about their potential toxicity, especially when modified with additives like melamine (M), remain largely unresolved. This study investigates the toxicological effects and underlying mechanisms of graphene oxide-melamine (GO-M) and carbon nanotube-melamine (CNT-M) nanoparticles in zebrafish (Danio rerio) embryos and larvae. To this end, developmental toxicity, phenotypic and behavioral changes, as well as histopathological and immunofluorescence alterations, were evaluated following acute exposure to GO-M and CNT-M nanoparticles at concentrations of 5, 10, and 20 mg/L. Results showed that both nanoparticles delayed larval hatching, particularly at higher concentrations (10 and 20 mg/L). Malformations were observed at 20 mg/L in the GO-M group and at 10 and 20 mg/L in the CNT-M group. Additionally, significant changes in larval length and eye area were observed at all concentrations for both nanoparticles. Behavioral assessments revealed that CNT-M exposure at 10 and 20 mg/L significantly impaired head sensorimotor reflexes, while all concentrations affected tail reflexes. In contrast, GO-M exposure did not significantly alter sensorimotor responses. These findings suggest differential toxic mechanisms and neurobehavioral effects of GO-M and CNT-M nanoparticles during early zebrafish development.Article Quaternary Ammonium Functionalized Cellulose for Bromate Ion Removal: Structural Insights and Efficacy Evaluation(Wiley, 2025) Koseoglu, Ecem; Senver, Buse Aleyna; Recepoglu, Yasar Kemal; Arar, OzgurThis study evaluates the potential of quaternary ammonium-modified cellulose as a biosorbent for bromate (BrO3-) removal from aqueous solutions. Elemental analysis and scanning electron microscopy (SEM) characterized the elemental composition and microstructural features of the biosorbent, whereas Fourier-transform infrared (FTIR) spectroscopy elucidated its molecular structure. Experimental results revealed that BrO3- removal efficiency increased with the biosorbent dose, achieving approximately 58%, 78%, and 90% removal with 0.025, 0.05, and 0.2 g of sorbent, respectively. The removal was pH-dependent, with efficiencies of 25%, 45%, and 76% at pH 2, 4, and 10, respectively, and the optimal removal was within the pH range of 6-8. Kinetic studies demonstrated rapid sorption, achieving 91% removal within 3 min. The Langmuir sorption isotherm model provided an excellent fit to the experimental data (R 2 = 0.9987), indicating a maximum sorption capacity of 9.40 mg/g. Thermodynamic analyses confirmed a spontaneous and endothermic sorption process (triangle G degrees = -8.11 kJ/mol; triangle H degrees = +2.22 kJ/mol). Desorption studies showed >= 99.9% efficiency using 0.1-M H2SO4 and NaCl, with NaCl selected as the preferred regenerant to minimize acid consumption. The biosorbent retained over 90% removal efficiency across three regeneration cycles. These findings highlight the potential of quaternary ammonium-modified cellulose as a sustainable and efficient material for BrO3- removal from water systems.Article Effect of Marination on the Formation of Polycyclic Aromatic Hydrocarbons in Grilled Vegetables(Wiley, 2025) Kacmaz Ozcetin, Sibel; Artok, LeventThe effect of marination on the formation of polycyclic aromatic hydrocarbons (PAH) in charcoal-grilled vegetables was studied. Various marinade ingredients, including apple cider vinegar, red grape vinegar, lemon juice, garlic powder, black pepper, and the food additive tert-butylhydroquinone (TBHQ) were applied to vegetable samples before charcoal grilling. The total phenolic content (TPC) and total antioxidant capacity (TAC) of each marinade ingredient were assessed for their contribution to PAH inhibition. A substantial decrease in PAH4 formation was observed in marinated vegetables. Red grape vinegar exhibited the strongest average inhibitory effect on total PAH4 formation (75%), followed by apple vinegar (68%), lemon juice (52%), garlic powder (34%), and black pepper (30%). Additionally, the TBHQ (67%) demonstrated a strong inhibitory effect, reducing total PAH4 formation by 67%. These findings offer valuable insights for reducing PAH levels in grilled vegetables and preventing their formation.Article Citation - WoS: 1Citation - Scopus: 1Exploring Sainfoin (Onobrychis Viciifolia) Seed Flour as a Sustainable Plant-Based Food: Germination-Induced Changes in Nutritional Quality, Anti-Nutritional Factors, Phenolic Content, Bioaccessibility, and in Vitro Toxicity(Wiley, 2025) Kaya, Havva Polat; Gungor, Sevde Nur; Tuncel, Nese Yilmaz; Sakarya, Fatma Betul; Andac, Ali Emre; Ozkan, Gulay; Tuncel, Necati BarisBackground and Objectives: Sainfoin is a drought-resistant perennial plant mainly used as animal feed, but its seeds remain underexplored as a food source. This study investigates the effects of germination on the nutritional quality of dehulled sainfoin seeds. Specifically, it examines changes in proximate composition, antinutrients (hydrocyanic acid, tannins, phytates, saponins, and trypsin inhibitors), in vitro starch digestibility, phenolic content, antioxidant capacity, and cytotoxicity. Findings: Germination significantly increased crude protein (up to 45%) and fat (up to 10%) contents. Despite low total starch (similar to 7%), 45-h germination reduced total digestible starch while increasing rapidly digestible starch. Antinutrient levels decreased significantly-tannins by 57%, phytates by 30%, saponins by 40%, and trypsin inhibitors by 29%-with the exception of hydrocyanic acid. Although total phenolics, flavonoids, and antioxidant capacity declined, their bioaccessibility improved. No cytotoxic effects were observed in either raw or germinated seeds. Conclusions: Germination improved the nutritional profile of sainfoin seeds by increasing protein and fat contents, while reducing most antinutrients. Despite a decrease in antioxidant levels, their bioaccessibility was enhanched. The absence of cytotoxic effects further supports the potential application of germinated sainfoin seeds in human nutrition. Significance and Novelty: Although few studies have focused on the green form of sainfoin, which is commonly used as livestock feed, this study reveals that sainfoin seeds offer substantial potential as food, with germination emerging as a simple and effective approach to improving their nutritional properties.Article Time-Dependent Effects of Low-Intensity Pulsed Ultrasound on Apoptosis and Autophagy in Malignant Melanoma Stem Cells(Wiley, 2025) Dikici, Omer; Ozdil, Berrin; Yesin, Taha Kadir; Dikici, Aylin; Adali, Yasemin; Aktug, HuseyinCancer stem cells (CSCs) in malignant melanoma contribute to therapeutic resistance and tumour recurrence. While low-intensity pulsed ultrasound (LIPUS) has been proposed as a non-invasive strategy to induce cell death, its effects on CSC-specific apoptotic and autophagic responses remain unclear. This study aimed to explore the time-dependent effects of LIPUS on apoptosis and autophagy in CD133+ melanoma CSCs and CD133- non-stem melanoma cells. Human melanoma cells (CHL-1) were sorted via FACS into CD133+ and CD133- populations. Cells were exposed to LIPUS (1 MHz, 20% duty cycle, 1 W/cm2) for 1, 5, and 10 min. Protein expression levels of Caspase-3, Caspase-8, mTOR, and LC3 were evaluated via immunofluorescence and quantified by image-based analysis. Both cell populations showed significant increases in Casp3, Casp8, mTOR, and LC3 intensities following LIPUS application. Notably, CD133+ cells exhibited delayed but sustained increases in Casp3 and LC3 expression, while CD133- cells responded more rapidly. mTOR activity demonstrated distinct temporal dynamics between the two groups, suggesting differential modulation of autophagy-related pathways. LIPUS triggers temporally distinct apoptotic and autophagic responses in melanoma CSCs and non-stem cancer cells. These findings suggest a potential therapeutic avenue to selectively disrupt CSC survival mechanisms using mechanical stimulation.Article Investigating the Effects of Functionalized Single Wall Carbon Nanotubes on the Cure Behavior of a Carbon/Epoxy Prepreg System by an Optimized Parameter Approach(Wiley, 2025) Oz, Murat; Uz, Yusuf Can; Tanoglu, Gamze; Tanoglu, Metin; Barisik, MuratCarbon/Epoxy composite materials are used in a wide range of applications due to their superior performance. However, their properties are strongly related to cross-linking reactions occurring during the curing process, and a prior estimation of curing parameters is the key to manufacturing the desired material. This study builds a mathematical model to solve the inverse kinetic problem based on differential scanning calorimetry data and later presents its use in curing experiments. The method derived (Gamze-Murat-Neslisah (GMN) approach) determines the pre-exponential and activation energy of the curing process. Later, an extended experimental study was performed. Functionalized single-wall carbon nanotubes (F-SWCNTs) were prepared by oxidizing their surface with carboxyl to enhance the dispersion of the nanoparticulates. The epoxy resin systems were modified with 0.05%, 0.1%, and 0.2% wt. F-SWCNTs, which were impregnated on carbon fibers (CFs). The curing behavior was studied, cure kinetic parameters were determined, and the thermal behavior was characterized. Differential scanning calorimetry (DSC) data sets for CF/epoxy prepregs containing F-SWCNTs were used for the verification of the proposed method. It was found that the GMN approach is in good agreement with the experimentally measured data for all kinetic parameters. The addition of F-SWCNTs increased the material's curing efficiency as the CNTs enhanced heat transport in composites, reducing the activation energy. The results obtained from the GMN algorithm were also found in good agreement with the well-known Kissinger-Akahira-Sunose (KAS) and Kissinger methods, while the current GMN method revealed itself as an accurate algorithm to obtain the activation energy.