PubMed İndeksli Yayınlar Koleksiyonu / PubMed Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/11147/7645
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Article Chloroaluminum Phthalocyanine Loaded Bovine Serum Albumin Nanoparticles as a Dual-Functional Nanoplatform for Sono-Photodynamic Cancer Therapy(Elsevier, 2026) Akyol-Karpuzcu, Cansu; Nartas, Eylem Doga; Calibasi-Kocal, Gizem; Akdogan, YasarChloroaluminum phthalocyanine (ClAlPc) loaded bovine serum albumin (BSA) nanoparticles (NPs) were synthesized as a dual-functional platform for photodynamic and sonodynamic therapies (PDT and SDT). ClAlPc loading did not disturb the morphology of the BSA NPs. Their spherical structure, with a size around 200 nm, was preserved upon ClAlPc loading (1 %w/w). Singlet oxygen productions in the presence of ClAlPc loaded BSA NPs or free ClAlPc were determined by ultraviolet absorption (UV-vis) spectroscopy and electron paramagnetic resonance (EPR) spectroscopy. While a slower rate of singlet oxygen formation rate after both PDT and SDT was detected by UV-vis measurements in the presence of ClAlPc loaded BSA NPs, EPR results showed a similar rate of singlet oxygen formation for both ClAlPc loaded BSA NPs and free ClAlPc. Confocal microscopy confirmed the efficient cellular uptake and perinuclear localization of the ClAlPc loaded BSA NPs in HCT-116 cancer cells. In vitro cytotoxicity studies demonstrated a dose and time dependent photo-and sonotoxic effects in the presence of ClAlPc loaded BSA. In particular, simultaneous application of light and ultrasound as sono-photodynamic therapy (SPDT) resulted in 15 % cell viability in the presence of ClAlPc loaded BSA NPs, which is much lower than individual PDT and SDT results, confirming the effect of the combination therapy on cell viability. In comparison, free ClAlPc reduced cell viability to 27 %. These findings suggest that ClAlPc loaded BSA NPs is a promising "one-for-two" nanoplatform for combined cancer therapy to reduce the limitations of both methods.Article 3D-Printed Soy Protein and Microalga Films: A Sustainable Approach with Antioxidant Functionality(Elsevier, 2026) Barekat, Sorour; Dogan, Buse; Uzuner, Sibel; Ubeyitogullari, AliThis study investigated the optimization and fabrication of soy protein isolate (SPI)-green microalga (MA) 3D-printed films. For optimizing 3D printing, the effects of MA concentration, nozzle size (0.52-0.81 mm), and speed (10-20 mm/s) were examined. The printed films were then dried, and color, mechanical properties, water vapor permeability, structure, and antioxidant activity were analyzed. All the formulations showed shear-thinning behavior and rapid recovery. The concentration of 3 % MA, nozzle size of 0.72 mm, and printing speed of 20 mm/s were selected as the optimized conditions for the best 3D printability. Compared with the control, their elongation at break decreased by more than 16 %, while puncture strength increased by over 12 %, and tensile strength rose by more than 40 %. Water vapor permeability decreased by more than 40 % with the addition of MA. The microstructure images and secondary structure confirmed the formation of a less porous and stronger gel network with an increase in MA concentration from 0 to 5 % (w/w). The antioxidant properties of SPI films also increased two-fold with the addition of MA. These findings highlight that the 3D-printed edible films with antioxidant properties could be used as an eco-friendly and nutritious alternative to petroleum-based films in food packaging.Article Magnetic Levitation-Based Determination of Single-Nuclei Density(Elsevier, 2026) Anil-Inevi, Muge; Sarigil, Oyku; Unal, Yagmur Ceren; Tekin, H. Cumhur; Mese, Gulistan; Ozcivici, EnginThe biophysical properties of cells and intracellular compartments provide critical insights into their structural and functional states, holding significant potential for biological and medical applications. Single-cell density has recently emerged as a promising biomarker in various research areas, including disease detection, making its precise measurement in biological samples an important analytical objective. Magnetic levitation offers significant advantages over traditional density detection techniques by enabling single-cell analysis rather than bulk measurements, providing precise quantification while preserving natural sample properties and eliminating the need for complex and expensive equipment. While magnetic levitation has been successfully applied to singlecell and cell-aggregate analysis, its use for subcellular compartments remains unexplored. Here, we demonstrate the first application of magnetic levitation technology for the density-based analysis of cell nuclei, a critical organelle essential for genomic preservation and organization. To accommodate the unique size and density characteristics of nuclei compared to whole cells, we systematically investigated appropriate paramagnetic agents, sample loading concentrations, and nuclear equilibrium times required for optimal levitation. We mapped density distributions of nuclei from different cell lines and conducted parallel assessments of cellular and nuclear density changes following cell cycle perturbations and treatments inducing cell death through distinct mechanisms. Our findings establish magnetic levitation as a powerful tool for subcellular density analysis, with potential applications in cell biology research and clinical diagnostics through improved understanding of subcellular physical parameters.Article Chain-Length Dependent and Synergistic Prebiotic Effects of Xylooligosaccharides and Xylan on the Fecal Microbiota of Mice in Vitro(Elsevier, 2025) Sabanci, Kevser; Gulec, Sukru; Buyukkileci, Ali OguzOligomeric and polymeric prebiotics differ in their structural complexity, which influences microbial accessibility and fermentation kinetics. This study investigated the microbial responses to xylooligosaccharides (XOS), xylan (XY), and their combinations in comparison with inulin (INU) using an in vitro model inoculated with BALB/c mice fecal microbiota. Temporal analyses over 48 h included substrate consumption, acid production, and changes in microbial diversity. XOS was rapidly fermented, yielding high acetate and lactate levels, whereas XY was utilized more slowly due to its polymeric structure. During XY fermentation, xylobiose (X2) and xylotriose (X3) accumulated transiently, suggesting a stepwise depolymerization and utilization mechanism. The XOS + XY mix showed enhanced prebiotic effect, producing the highest amount of acid (151.8 mmol/L) and notably promoted the simultaneous enrichment of Bifidobacterium (12.5-fold), Bacteroides (8.85-fold), and Lactobacillus (14.9-fold) species compared to individual treatments These findings demonstrate that coadministered XOS and XY highlights the potential for designing tailored prebiotic formulations to optimize microbiota modulation, with potential relevance for human health.Article Lipid Monolayer Composition and Production Efficiency in DSPC/PEG40St Microbubbles for Ultrasound Applications(Elsevier, 2025) Kilic, Sevgi; Ozdemir, EkremLipid-coated microbubbles are widely used as ultrasound contrast agents (UCAs) and are being developed as carriers for drug and gene delivery. These microbubbles typically consist of an inert gas core and a stabilizing monolayer shell of phospholipid and a PEGylated emulsifier. In practice, a 9:1 M ratio of DSPC (a saturated phospholipid) to PEG-40-stearate (PEG40St) is conventionally used, under a long-standing assumption that the final composition of the microbubble shell is identical to the initial mixture composition. In this study, we tested that assumption over a wide range of DSPC/PEG40St ratios. Using sonication-based fabrication, we prepared microbubble suspensions with PEG40St fractions from 10 % up to 90 %. We then quantified the shell composition by proton nuclear magnetic resonance (1H NMR) and measured microbubble yield. Contrary to expectation, the PEG40St content in the bubble shells lower than PEG40St added, indicating selective exclusion or "squeezing out" of PEG40St during formation. Only about 4-6 % of the total lipid mixture ended up in the bubble shells and the rest remained as excess in the sub-phase. Thus, 94-96 % of the costly lipid/emulsifier was wasted in the production process. These results overturn the conventional assumption and highlight a critical inefficiency such that substantial amounts of lipid and PEG40St were lost during production, and the bubble yields were low. The findings have important implications for microbubble manufacturing, suggesting that alternative formulations or other production methods are needed to improve efficiency, and thus reduce costs.Article Citation - WoS: 1Citation - Scopus: 1Biophysical Assessment of Protein Stability in Ethanol-Stressed Environments via UV Absorption and Fluorescence Spectroscopies(Elsevier, 2026) Akyuz, Ersed; Vorob'ev, Mikhail M.; Guler, GunnurMaintaining the structure and functionality of proteins is crucial in applications ranging from food preservation to pharmaceutical formulation. Ethanol, while commonly used as a solvent and preservative, can induce structural changes in proteins depending on its concentration and the specific structure of the protein itself. This study investigates the structural effects of ethanol on three types of model proteins, namely bovine serum albumin (BSA), beta-Lactoglobulin (beta-Lg), and beta-Casein (beta-Cn), by using UV-Vis spectroscopy and fluorescence spectroscopy. The conformational responses of proteins in water-EtOH solutions of various ethanol concentrations (0-10 %, v/v) were analyzed through absorbance and emission spectral changes. At increasing ethanol concentration, UV absorption data showed distinct protein-dependent spectral changes. beta-Lg and beta-Cn exhibited strong hypochromism (an absorbance decrease of similar to 25 %) and red-shifting at 222 nm and 220 nm, respectively, indicating partial unfolding and solvent exposure of aromatic residues. BSA demonstrated subtle changes, and consistent quenching in fluorescence with a continuous blue-shifting to 330 nm, suggesting a moderate overall stability and local rearrangements in its structure. beta-Cn exhibited red-shifted fluorescence and quenching, reflecting its flexible, disordered structure and heterogeneous response to solvent conditions. Statistical analysis revealed that while fluorescence spectroscopy was highly sensitive to the intrinsic differences between proteins (p < 0.001), the ethanol-induced conformational changes were too subtle to be detected as a statistically significant treatment effect. The consistency of these trends indicates a rational underlying mechanism of interaction. This reflects the subtle nature of the effect at the tested concentrations rather than the absence of an effect. Moreover, these results unveil the protein-specific effects of ethanol and strongly emphasize the importance of solvent composition in maintaining protein integrity. Ethanol concentrations up to 5 % may offer protein stability whereas high ethanol levels (>= 5-10 %) promote structural perturbations. These results will be useful for both basic scientific research, such as biophysical studies and the advancement of optical techniques, and various industrial uses.Article Techno-Functional and Antioxidant Properties of Chickpea Proteins Interacted with Green Tea Phenolics-Exploring Benefits for Gel and Emulsion-Based Vegan Foods(Elsevier, 2025) Kavur, Pelin Baris; Sahin, Damla Oyku; Cavdaro Glu, Elif; Buyuk, Miray; Cakitli, Gamze; Hamzaoglu, Fatmagul; Yemenicioglu, AhmetThis study aimed at exploiting protein-polyphenol interactions to enhance techno-functional and antioxidant properties of chickpea proteins. For this purpose, prior to protein extraction, chickpeas were rehydrated in green tea infusion (GTI). Extracted chickpea proteins (CPCGTI) contained free (90.7 mu g/g) and bound (32.0 mu g/g) green tea phenolics (e.g., gallic acid, catechin, epigallocatechin 3-gallate, epicatechin 3-gallate). A close association between chickpea protein and green tea polyphenols was determined considering pH-solubility profile of CPCGTI. CPCGTI showed superior antioxidant potential (6.5-fold), water/oil absorption capacity (1.4-1.5-fold), and gel firmness than control chickpea protein (CPCC). Edible films of CPCGTI also showed 2.4-fold higher antioxidant capacity than those of CPCC. CPCGTI and CPCC showed similar SDS-PAGE patterns, but different alpha-helix and beta-sheet contents evaluated by FTIR. CPCGTI gave thick, creamy and stable mayonnaise while CPCC failed to form mayonnaise. The coconut milk pudding with CPCGTI showed better gelation than that with CPCC. However, foods with CPCGTI had a darker color than those with CPCC. CPCGTI is a novel, highly functional ingredient for manufacturing plant-based food and edible packaging.Article Citation - WoS: 1Citation - Scopus: 1Peptide-Functionalized Hydrocolloid Bioink for 3D Bioprinting in Dental Tissue Engineering(Elsevier, 2025) Guner, Elif; Yildirim-Semerci, Ozum; Altan, Zeynep; Arslan-Yildiz, AhuDeveloping biomimetic peptide-based biomaterials has utmost importance to enhance mineralization offering an innovative approach for dental tissue regeneration. This study comprises development and characterization of a novel peptide-based hybrid bioink for dental tissue engineering applications by integrating P11-4 peptide and Gelatin (Gel) into glucuronoxylan-based quince seed hydrocolloid (QSH). Combining polysaccharide and peptide-based hydrogels enhanced cell adhesion and mineralization. Morphological analysis showed that P11-4 increased porosity, while rheological tests confirmed that QSH/Gel/P11-4 bioink has tunable viscosity, which is suitable for 3D bioprinting. Optimized bioprinting parameters were determined to be 25G nozzle diameter, 10 mm/s speed of movement, 0.1 mm layer height, and pressure values of 9.0 and 7.0 psi for QSH/Gel and QSH/ Gel/P11-4, respectively. Moreover, the addition of P11-4 significantly increased protein adsorption without affecting swelling capacity. 3D cell culture studies were conducted using SaOS-2 (human osteosarcoma) cells, then biocompatibility, high cell viability, favored adhesion, and proliferation were confirmed by Live/Dead and MTT assays. Alizarin Red Staining (ARS) and EDX analysis verified that P11-4 promoted mineral deposition by increasing Calcium (Ca2+) accumulation in QSH/Gel/P11-4 scaffolds, suggesting that developed bioink can mimic native ECM microenvironment for dental tissue. Overall, the developed hybrid bioink shows superior printability and bioactivity, which makes it a promising material for 3D bioprinting applications in dental tissue engineering.Article Beyond Traditional Dentistry: How Organoids and Next-Gen Hydrogels Are Redesigning Dental Tissue Regeneration(Elsevier, 2026) Yilmaz-Dagdeviren, Hilal Deniz; Arslan, Yavuz EmreDental tissue regeneration has advanced rapidly with the development of bioengineered hydrogels and organoid technologies. In this review, multifunctional hydrogels are examined as biomimetic platforms with osteoinductive, adhesive, angiogenic, antimicrobial, and immunomodulatory properties tailored to enamel, dentin-pulp complex, periodontal ligament, and alveolar bone repair. Incorporation of bioactive molecules, including growth factors, bioceramics, antioxidants, and immune-modulating agents, has been reported to enhance tissue-specific regeneration while mitigating infection and inflammation. Stimuli-responsive designs have been utilized to enable spatiotemporally controlled delivery and degradation. Immunomodulatory hydrogels also have been shown to direct macrophage polarization, regulate T-cell infiltration, and promote matrix remodeling. Furthermore, organoid models supported by hydrogels have been employed to replicate dental tissue architecture, guide lineage-specific differentiation, and provide reproducible, physiologically relevant platforms for drug screening and developmental studies. Emerging strategies such as microfluidic organoid-on-chip systems and mechanically stimulated cultures are noted for their potential to provide more physiologically relevant models. Early clinical studies involving hydrogel-based scaffolds and stem cell constructs are discussed, indicating growing translational potential. Overall, these developments highlights that how advanced hydrogels and organoid systems can contribute to a shift from conventional restorative methods toward tissue engineering-based regenerative therapies.Article Citation - WoS: 1Citation - Scopus: 1A Green Route to Albumin/Albumin Polyelectrolyte Complex Nanoparticles in Water With High Drug Loading for Drug Delivery(Elsevier, 2025) Sozer-Demirdas, Sumeyra Cigdem; Erez, Ozlem; Cakan-Akdogan, Gulcin; Akdogan, YasarA polyelectrolyte complex (PEC) formation offers a simple and green approach to obtaining albumin nanoparticles (NPs) without the use of organic solvents, crosslinkers and specialized equipment. The prepared cationic albumin proteins interact with anionic albumin proteins to form albumin PEC NPs (110 nm) with +37 mV surface zeta potential. Furthermore, albumin PEC NPs preparation in water alone achieves chlorambucil (CHL) loading up to 17 times higher than the conventional desolvation method, largely due to the elimination of drug loss to organic solvents. CHL loaded albumin PEC NPs also decreased the cell viability (Huh-7) to 44 % within 24 h. This study demonstrates that high drug-loaded albumin NPs can be alternatively synthesized by using albumin polyelectrolyte properties, and applied in drug delivery applications.