Scopus İndeksli Yayınlar Koleksiyonu / Scopus Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/11147/7148
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Article Application of 3D Cell Culture Techniques in Nanotoxicology: How Far Are We(Springer, 2026) Shakeri, Raheleh; Mirjalili, Seyedeh Zohreh; Karakus, Ceyda Oksel; Safavi, MalihehInvestigation of toxicological profile and possible side effects of engineered nanomaterials (ENMs) is of high importance. Historically, two-dimensional (2D) cell culture was used to study the toxicity of the ENMs, but due to their inability to simulate in vivo cell behavior, three-dimensional (3D) cell culture systems have been developed. Nanotoxicity studies initiate with in vitro experiments and continue with in vivo studies, which are very challenging and sometimes accompanied by conflicting data due to the in vitro-in vivo gap. Thus, scientists are turning their attention to microfabrication techniques and engineered systems "called organ-on-a-chips", which act as an intermediate between in vivo and in vitro systems. The present account tries to review the classical study models and suitably cover the emerging 3D culture models including scaffold-free and scaffold-based 3D cell cultures, 3D co-culture with direct contact and without cell-cell contact methods as well as microfluidic-based tissue chips and organoids. Overall, this review aims to give readers a better insight about the ENMs' toxicology and fill the gaps between the knowledge and practical techniques. Hopefully, the presented information will resolve the issues of 2D in vitro cultures and display the clinically relevant responses to the concerns of therapeutic ENMs.Article Storage Protein Allergen Sensitization Patterns in Children: Insights from Multiplex Microarray Profiling and Hierarchical Clustering(Wiley, 2025) Caka, Canan; Ozcivici, Engin; Karakus, Ceyda Oksel; Sekerel, Bulent EnisBackground Storage proteins (SPs), including 2S albumins, vicilins, and legumins, are key allergenic molecules (AMs) of peanuts, tree nuts (TNs), and sesame. Their structural stability contributes to allergenicity and sensitization. This study explored SP AM clustering patterns and evaluated the test performance of multiplex microarray (MM) testing in a pediatric cohort. Methods We retrospectively analyzed 350 children (median age: 3.7 years) with detectable SP sensitizations (>= 0.1 kU(A)/L) using the ALEX(2) MM platform. Sensitization interrelationships were analyzed using correlation heatmaps, hierarchical clustering (HC), dimensionality reduction, and feature elimination. Predictive utility was assessed through ROC curve analysis at different sensitization cut-offs (>0.1 and >0.3 kU(A)/L) and total IgE thresholds (>0, >20, and >50 kU/L). Results HC identified a broad SP cluster spanning peanuts, TNs, sesame, poppy seed, and buckwheat. Strong correlations and early HC linkages suggested extensive cross-sensitization (e.g., Ana o 3-Pis v 1 and Jug r 4-Cor a 9), alongside evidence of co-sensitization and molecular spreading. Unexpected clustering of structurally dissimilar peanut and pistachio AMs pointed to shared epitopes and/or cross-contamination. 2S albumins (Ara h 2, Cor a 14, Jug r 1, Ana o 3, and Ses i 1) were most predictive for clinical reactivity. Lower cut-offs and exclusion of patients with low total IgE improved test performance. Alpha-hairpinin (Pap s 2S albumin) showed potential as specific markers. Conclusions MM testing enables detailed SP sensitization profiling. Cluster-based interpretation may clarify cross- vs. co-sensitization, supporting informed clinical decisions. Use of recombinant AMs and IgE stratification may further enhance MM utility in food allergy diagnostics.Article Citation - WoS: 3Citation - Scopus: 3Design, Synthesis, Characterization and Biological Evaluation of Cobalt-Ferrite Nanoparticles for Biomedical Applications(Elsevier, 2025) Esmer, Ecem Fatma; Bilgi, Eyup; Dincay, Selin Cesmeli; Sakalli, Tugce; Karakus, Ceyda OkselCobalt-Ferrite nanoparticles (CF NPs) are increasingly used in biomedical applications due to their unique magnetic properties and biocompatibility. In this study, CF NPs were synthesized via co-precipitation, both in the presence and absence of oleic acid (OA) as a surfactant. Plackett-Burman Design was employed to study the influence of reaction conditions on the particle size distribution of bare and OA-coated CF NPs. Representative bare and OA-coated CF NP samples were characterized for morphology, composition, thermal stability, and optical and magnetic properties using TEM, XRD, FTIR, TGA, UV-Vis, and VSM. The highest saturation magnetization value (similar to 44 emu/g) was observed for bare CF NPs of smaller sizes. MTT assay results indicated that none of the tested samples showed significant cytotoxicity at the concentrations tested (1, 10, and 100 mu g/mL), except for the bare CF NPs, which reduced viability of A549 cells to approximately 50 % following 72-hour exposure at 100 mu g/mL. Following incubation in a cell culture medium for 48 h, proteins bound to the surface of CF NPs were analyzed using SDS-PAGE, revealing bovine serum albumin, apolipoprotein A-I and fibronectin as the most abundant proteins across samples. Overall, OA-coating slightly improved colloidal stability and reduced cytotoxicity, without significantly compromising the magnetic or protein-binding properties.Article Citation - Scopus: 1Investigating Early-Stage Mineralization Behavior and Bioactivity of Acid-Free Bioactive Glass 45s5 With Enhanced Dissolution Kinetics(Springer, 2025) Tuncer, Melisa; Yucesoy, Deniz T.; Karakus, Ceyda OkselNanostructured bioactive glass (BG) was synthesized through an acid-free sol-gel route (bioglass-AF) and the conventional acid-catalyst sol-gel process (bioglass-AC). The aim here is to eliminate the risk of residual acidic components in the BG while enhancing its functionality through nano-scale propduction. Scanning electron microscopy revealed the presence of highly porous structures and dense agglomerates composed of particles with a mean diameter of 45 nm in both samples. Bioglass-AC and bioglass-AF had specific surface areas of 1.48 m(2)/g and 2.73 m(2)/g, respectively, with an average pore size of similar to 5 nm. Faster mineralization kinetics were evident in bioglass-AF, compared to bioglass-AC, in Hepes-buffered salt solution. Following 14 days of immersion in artificial saliva, bioglass-AC and bioglass-AF lost 16% and 20% of their initial weight, respectively, confirming their bioactivity. None of the synthesized BGs stimulated cell growth up to 24 h but longer exposure to moderate concentrations (1.25 and 2.5 mg/mL) of bioglass-AF significantly enhanced cell viability, reaching 170% at 48 h. Overall, the comparative in vitro investigations proved that nano-structured 45S5 bioglass powders with improved mineralization and dissolution kinetics can be produced with an acid-free route, eliminating the risk of residual acidic components in the final product.Article Proliferative Effects and Cellular Uptake of Ceramic Nanoparticles in Cancer and Normal Cells(Univ Chemistry & Technology, Prague, 2024) Cesmeli, Selin; Tomak, Aysel; Winkler, David A.; Karakus, Ceyda OkselThe high biocompatibility, wear resistance, and high surface area-to-volume ratios of calcium phosphate (CaP) nanoparticles make them materials of great interest for a very broad range of medical applications, such as dentistry, drug delivery, biomedical imaging, gene transfection and silencing, biomedical imaging, immunisation, and bone substitution. While their use as an enamel remineralisation agent, a bone substitution material, an implant coating, and drug/gene delivery agents is widely approved by the regulating bodies, insufficient attention has been paid to the interactions of CaP-based nanoparticles with cells and organs once in the bloodstream and distributed through the body. Here, three different CaP-based nanoparticles (CP: calcium phosphate, TCP: tricalcium phosphate, and HAp: hydroxyapatite) were examined for the proliferative effects, oxidative damage potential, and cellular uptake in the human embryonic kidney (HEK293) and pancreatic cancer (Panc-1) cell lines. The physicochemical properties of the nanoparticles were characterised by Teller analysis, and X-ray diffraction spectroscopy. Maximum proliferative effects were generated by 400 mu g center dot ml-1 TCP (220 %) in HEK293 cells. Interestingly, although CP nanoparticles had the highest reactive oxygen species formation capacity in the HEK293 cells, they exhibited the lowest proliferative effects and a relatively low internalisation rate, suggesting a minimal correlation between the cellular uptake level and oxidative potential.Article Citation - WoS: 1Citation - Scopus: 1Green Synthesis of Silver Nanoparticles Using Plant Extract Blends and Its Impact on Antibacterial and Biological Activity(World Scientific Publ Co Pte Ltd, 2024) Ozturk, Selin Naz; Tomak, Aysel; Karakus, Ceyda OkselThere is a strong interest in using green resources for synthesizing nanoparticles (NPs) of industrial and biomedical utility in a way to maintain desired material properties throughout use while not inducing any harmful effects. The use of various plant extracts as reducing, capping, or stabilizing agents is widely attempted in green nanotechnology. However, very little has been explored about incorporating plant extract blends into green NP synthesis routes. Here, we used the combination of tea and olive leaf extracts for the synthesis of silver NPs and evaluated the advantages it provided over both chemical and single-plant-mediated synthesis routes. Four different reducing agents (tannic acid, black tea leaves extract, olive leaves extract and their blend) were used to synthesize silver NPs (Ag NP) from silver nitrate (AgNO3). The synthesized Ag NP was characterized by scanning electron microscopy (SEM), dynamic light scattering (DLS), and ultraviolet-visible (US-Vis) spectroscopy. The antimicrobial properties of Ag NP were assessed against Escherichia coli (E. Coli) and Staphylococcus aureus (S. Aureus) using the colony-forming unit (CFU) assay and the minimum inhibitory concentration (MIC) assay. The cytotoxic potential of Ag NP on human colorectal adenocarcinoma (Caco-2) cells was assessed by the WST-1 assay. Results showed that Ag NP synthesized using plant extract mixtures had a primary particle size of 40nm and were very effective antibacterial agents, with the MIC values ranging from 5 mu g/mL to 10 mu g/mL. While the particle size obtained in chemical synthesis was slightly lower, the resultant Ag NP did not serve as an effective antibacterial agents at low doses. Further understanding of how best to integrate extracts of different plants into green NP synthesis routes will enable wider and safer biomedical applications.