Scopus İndeksli Yayınlar Koleksiyonu / Scopus Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/11147/7148
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Article Investigation of Few-Layer Graphene-Ubiquitin Interactions with Optical Spectroscopy Techniques(MDPI, 2025) Gencay, Burcu; Guler, GunnurUnderstanding the molecular mechanisms of protein-nanoparticle interactions is crucial for enabling the development of new applications in biomedicine and nanotechnology. Ubiquitin, an important and structurally small functional protein, plays a central role in numerous cellular processes. Therefore, in the current study, we focused on the few-layer graphene (FLG)-Ubiquitin complexes formed by exfoliating FLG structures using only water. Optical spectroscopic techniques (Raman, FT-IR, UV-Vis and circular dichroism) were employed to investigate these complexes on the molecular level. Overall, both CD and FT-IR data reveal that the formation of the FLG-Ubiquitin complexes occurred without inducing disordered structures in the protein. Based on the existence of a blue shift (hypsochromic shift) in the UV-Vis data, the presence of a single tyrosine and two phenylalanine residues in ubiquitin enables the detection of FLG-induced micro-environmental changes, particularly influencing the protein's beta-sheet and alpha-helix structures. The CD spectral results and CDPro quantitative estimations are in line with ATR FT-IR results, confirming the absence of disordered structure formation while altering the protein's chirality. UV-Vis and CD spectroscopy results revealed concentration-dependent trends consistent with FLG-protein interactions that preserve the overall protein structure. This study has potential applications in both academic research and practical usage, particularly in biomedicine and nanotechnology specifically for FLG.Article Comparative Stability of Synthetic and Natural Polymeric Micelles in Physiological Environments: Implications for Drug Delivery(MDPI, 2025) Polat, Hurriyet; Eren, Merve Cevik; Polat, Mehmet; Koss, Kyle M.; Polat, Onur K.Polymeric micelles are widely studied as nanocarriers for hydrophobic drugs, yet their structural stability under physiological conditions remains a major limitation. This review provides a comparative evaluation of synthetic and natural polymeric micelles with a focus on their stability under dilution and in protein-rich environments. The discussion integrates thermodynamic and kinetic factors governing micelle integrity and examines how molecular composition, hydrophobic segment length, and core-shell modifications influence disintegration behavior. While synthetic micelles commonly collapse below their critical micelle concentration during intravenous administration, natural polymeric micelles, such as those derived from chitosan, alginate, or heparin, exhibit improved resistance to dilution but remain vulnerable to protein-induced destabilization. Strategies such as core or shell cross-linking, surface functionalization, and natural polymer coatings are reviewed as promising approaches to enhance circulation stability and controlled drug release. The work provides a framework for designing micellar systems with balanced biocompatibility, biodegradability, and robustness suitable for clinical drug-delivery applications.Article A Hybrid Control Scheme for Backdriving a Surgical Robot About a Pivot Point(MDPI, 2025) Dede, Mehmet Ismet Can; Kurt, A. N. Olcay; Deniz, Mehmet FiratAn incision point acts as the pivot point when a minimally invasive surgery procedure is applied. The assistive robot arms employed for such operation must have the capability to perform a remote center of motion (RCM) at this pivot point. Other than designing RCM mechanisms, a common practice is to use a readily available spatial serial robot arm and control it to impose this RCM constraint. When this assistive robot is required to be backdriven by the surgeon, the relation between the interaction forces/moments and the motion with RCM constraint becomes challenging. This paper carefully formulates a hybrid position/force control scheme for this relationship when any readily available robot arm that is coupled with a force/torque sensor is used for an RCM task. The verification of the formulation is carried out on a readily available robot arm by implementing the additional constraints that are derived from a surgical robot application.Article Citation - WoS: 15Citation - Scopus: 16Formulation of Gluten-Free Cookies Utilizing Chickpea, Carob, and Hazelnut Flours Through Mixture Design(MDPI, 2023) Doğruer, Ilgın; Başer, Filiz; Güleç, Şükrü; Tokatlı, Figen; Özen, BanuLegume flours, which offer high nutritional quality, present viable options for gluten-free bakery products. However, they may have an objectionable flavor and taste for some consumers. In this study, it was aimed to improve the gluten-free cookie formulation by incorporating carob and hazelnut flours to pre-cooked chickpea flour and to investigate the techno-functional properties of the formulated cookies. The flours used in the formulations were assessed for their chemical and physical properties. This study employed a mixture design (simplex-centroid) to obtain the proportions of the flours to be used in the cookie formulations. The rheological characteristics of the doughs and the technological attributes of the baked cookies were determined. The addition of the hazelnut and carob flours had the overall effect of reducing the rheological characteristics of the cookie doughs. Furthermore, the textural attribute of the hardness of the baked cookies decreased as the ratio of hazelnut flour in the formulations was raised. The analysed results and sensory evaluation pointed to a formulation consisting of 30% pre-cooked chickpea/30% carob/30% hazelnut flours, which exhibited improved taste and overall acceptability scores. A total of 16.82 g/100 g of rapidly digestible starch, 5.36 g/100 g of slowly digestible starch, and 8.30 g/100 g of resistant starch exist in this particular cookie. As a result, combinations of chickpea, hazelnut, and carob flours hold promise as good alternatives for gluten-free cookie ingredients and warrant further exploration in the development of similar products.Article Citation - WoS: 16Citation - Scopus: 17Techno-Functional and in Vitro Digestibility Properties of Gluten-Free Cookies Made From Raw, Pre-Cooked, and Germinated Chickpea Flours(MDPI, 2023) Doğruer, Ilgın; Çoban, Başak; Başer, Filiz; Güleç, Şükrü; Özen, BanuChickpea flour, which is produced in various forms, has high protein and fiber content; therefore, it can be a good ingredient for gluten-free cookies. The objective of this study was to investigate and compare the properties of cookies formulated using raw (RCF), cooked (CCF), and germinated (GCF) chickpea flours. The techno-functional properties of these flours were determined, and scanning electron microscope images and mid-infrared spectra were obtained. The rheological properties of cookie doughs were measured along with their mid-infrared spectra. Baked cookies were analyzed for their technological properties as well as their in vitro digestion properties. Sensory analysis was also performed for all the cookies. The most significant difference among the flours was observed in their water retention capacity, and CCF had 119.7% higher water retention capacity compared to RCF. The dough made with CCF had quite different rheological properties from the others. The cookies baked with GCF had the highest baking loss and spread ratio. The CCF-containing cookies had the hardest structure. The cookies made from RCF had a higher resistant starch content followed by the cookies with GCF. All the cookies had similar scores in all aspects tested in the sensory analysis. The use of three different forms of chickpea flour in cookie formulations resulted in products with very different properties; however, their overall acceptability levels were close.Article Citation - WoS: 2Citation - Scopus: 3High-Pressure Processing of Traditional Hardaliye Drink: Effect on Quality and Shelf-Life Extension(MDPI, 2023) Atmaca, Bahar; Demiray, Merve; Akdemir Evrendilek, Gülsün; Bulut, Nurullah; Uzuner, SibelHardaliye, as one of the oldest and lesser known traditional beverages, is produced using red grape pomace from wine production. This drink production is achieved through lactic acid fermentation, with the addition of sour cherry leaves and mustard seeds-either heat-treated, grinded, or whole-in various concentrations. Hardaliye has a very short shelf life; thus, efforts have recently been made to process hardaliye with novel processing technologies in order to achieve shelf-life extension. Therefore, the high-hydrostatic-pressure (HHP) processing of hardaliye was performed to determine its impact on important properties, including in microbial inactivation and shelf-life extension, with respect to a Box-Behnken experimental design. Maximum log reductions of 5.38 & PLUSMN; 0.6, 5.10 & PLUSMN; 0.0, 5.05 & PLUSMN; 0.2, and 4.21 & PLUSMN; 0.0 with HHP were obtained for Brettanomyces bruxellensis, total mesophilic aerobic bacteria, Lactobacillus brevis, and total mold and yeast, respectively. The processing parameters of 490 MPa and 29 & DEG;C for 15 min were found as the optimal conditions, with the response variables of an optical density at 520 nm and the inactivation of L. brevis. The samples processed at the optimal conditions were stored at both 4 and 22 & DEG;C for 228 d. While the non-treated control samples at 4 and 22 & DEG;C were spoiled at 15 and 3 d, the HHP-treated samples were spoiled after 228 and 108 d at 4 and 22 & DEG;C, respectively.Article Citation - WoS: 21Citation - Scopus: 22High-Dose Exposure To Polymer-Coated Iron Oxide Nanoparticles Elicits Autophagy-Dependent Ferroptosis in Susceptible Cancer Cells(MDPI, 2023) Lomphithak, Thanpisit; Helvacıoğlu, Selin; Armenia, Ilaria; Keshavan, Sandeep; Ovejero, Jesus G.; Baldi, Giovanni; Ravagli, Costanza; Grazú, Valeria; Fadeel, BengtFerroptosis, a form of iron-dependent, lipid peroxidation-driven cell death, has been extensively investigated in recent years, and several studies have suggested that the ferroptosis-inducing properties of iron-containing nanomaterials could be harnessed for cancer treatment. Here we evaluated the potential cytotoxicity of iron oxide nanoparticles, with and without cobalt functionalization (Fe2O3 and Fe2O3@Co-PEG), using an established, ferroptosis-sensitive fibrosarcoma cell line (HT1080) and a normal fibroblast cell line (BJ). In addition, we evaluated poly (ethylene glycol) (PEG)-poly(lactic-co-glycolic acid) (PLGA)-coated iron oxide nanoparticles (Fe3O4-PEG-PLGA). Our results showed that all the nanoparticles tested were essentially non-cytotoxic at concentrations up to 100 mu g/mL. However, when the cells were exposed to higher concentrations (200-400 mu g/mL), cell death with features of ferroptosis was observed, and this was more pronounced for the Co-functionalized nanoparticles. Furthermore, evidence was provided that the cell death triggered by the nanoparticles was autophagy-dependent. Taken together, the exposure to high concentrations of polymer-coated iron oxide nanoparticles triggers ferroptosis in susceptible human cancer cells.Article Citation - WoS: 9Citation - Scopus: 8Astragalus Saponins, Astragaloside Vii and Newly Synthesized Derivatives, Induce Dendritic Cell Maturation and T Cell Activation(MDPI, 2023) Yakuboğulları, Nilgün; Çağır, Ali; Bedir, Erdal; Sağ, DuyguAstragaloside VII (AST VII), a triterpenic saponin isolated from Astragalus species, shows promise as a vaccine adjuvant, as it supported a balanced Th1/Th2 immune response in previous in vivo studies. However, the underlying mechanisms of its adjuvant activity have not been defined. Here, we investigated the impact of AST VII and its newly synthesized semi-synthetic analogs on human whole blood cells, as well as on mouse bone marrow-derived dendritic cells (BMDCs). Cells were stimulated with AST VII and its derivatives in the presence or absence of LPS or PMA/ionomycin and the secretion of cytokines and the expression of activation markers were analyzed using ELISA and flow cytometry, respectively. AST VII and its analogs increased the production of IL-1β in PMA/ionomycin-stimulated human whole blood cells. In LPS-treated mouse BMDCs, AST VII increased the production of IL-1β and IL-12, and the expression of MHC II, CD86, and CD80. In mixed leukocyte reaction, AST VII and derivatives increased the expression of the activation marker CD44 on mouse CD4+ and CD8+ T cells. In conclusion, AST VII and its derivatives strengthen pro-inflammatory responses and support dendritic cell maturation and T cell activation in vitro. Our results provide insights into the mechanisms of the adjuvant activities of AST VII and its analogs, which will be instrumental to improve their utility as a vaccine adjuvant. © 2023 by the authors.Article Citation - WoS: 7Citation - Scopus: 11Applications of Uv–visible, Fluorescence and Mid-Infrared Spectroscopic Methods Combined With Chemometrics for the Authentication of Apple Vinegar(MDPI, 2023) Çavdaroğlu, C.; Özen, B.Spectroscopic techniques as untargeted methods have great potential in food authentication studies, and the evaluation of spectroscopic data with chemometric methods can provide accurate predictions of adulteration even for hard-to-identify cases such as the mixing of vinegar with adulterants having a very similar chemical nature. In this study, we aimed to compare the performances of three spectroscopic methods (fluorescence, UV–visible, mid-infrared) in the detection of acetic-acid/apple-vinegar and spirit-vinegar/apple-vinegar mixtures (1–50%). Data obtained with the three spectroscopic techniques were used in the generation of classification models with partial least square discriminant analysis (PLS-DA) and orthogonal partial least square discriminant analysis (OPLS-DA) to differentiate authentic and mixed samples. An improved classification approach was used in choosing the best models through a number of calibration and validation sets. Only the mid-infrared data provided robust and accurate classification models with a high classification rate (up to 96%), sensitivity (1) and specificity (up to 0.96) for the differentiation of the adulterated samples from authentic apple vinegars. Therefore, it was concluded that mid-infrared spectroscopy is a useful tool for the rapid authentication of apple vinegars and it is essential to test classification models with different datasets to obtain a robust model. © 2023 by the authors.Article Citation - WoS: 3Citation - Scopus: 3Her2-Specific Peptide (ltvspwy) and Antibody (herceptin) Targeted Core Cross-Linked Micelles for Breast Cancer: a Comparative Study(MDPI, 2023) Bayram, N.N.; Ulu, G.T.; Abdulhadi, N.A.; Gürdap, S.; İşoğlu, İ.A.; Baran, Yusuf; İşoğlu, S.D.This study aims to prepare a novel breast cancer-targeted micelle-based nanocarrier, which is stable in circulation, allowing intracellular drug release, and to investigate its cytotoxicity, apoptosis, and cytostatic effects, in vitro. The shell part of the micelle is composed of zwitterionic sulfobetaine ((N-3-sulfopropyl-N,N-dimethylamonium)ethyl methacrylate), while the core part is formed by another block, consisting of AEMA (2-aminoethyl methacrylamide), DEGMA (di(ethylene glycol) methyl ether methacrylate), and a vinyl-functionalized, acid-sensitive cross-linker. Following this, a targeting agent (peptide (LTVSPWY) and antibody (Herceptin®)), in varying amounts, were coupled to the micelles, and they were characterized by 1H NMR, FTIR (Fourier-transform infrared spectroscopy), Zetasizer, BCA protein assay, and fluorescence spectrophotometer. The cytotoxic, cytostatic, apoptotic, and genotoxic effects of doxorubicin-loaded micelles were investigated on SKBR-3 (human epidermal growth factor receptor 2 (HER2)-positive) and MCF10-A (HER2-negative). According to the results, peptide-carrying micelles showed a higher targeting efficiency and better cytostatic, apoptotic, and genotoxic activities than antibody-carrying and non-targeted micelles. Also, micelles masked the toxicity of naked DOX on healthy cells. In conclusion, this nanocarrier system has great potential to be used in different drug-targeting strategies, by changing targeting agents and drugs. © 2023 by the authors.
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