PubMed İndeksli Yayınlar Koleksiyonu / PubMed Indexed Publications Collection

Permanent URI for this collectionhttps://hdl.handle.net/11147/7645

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Now showing 1 - 10 of 258
  • Article
    Application of 3D Cell Culture Techniques in Nanotoxicology: How Far Are We
    (Springer, 2026) Shakeri, Raheleh; Mirjalili, Seyedeh Zohreh; Karakus, Ceyda Oksel; Safavi, Maliheh
    Investigation 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
    Linking RNA Methylation to Structure: A Biophysical Perspective
    (Wiley, 2026) Akgul, Bunyamin; Guler, Gunnur; Saglam, Buket; Akkus, Onur; Akcaoz-Alasar, Azime
    Recent 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
    Investigation of Few-Layer Graphene-Ubiquitin Interactions with Optical Spectroscopy Techniques
    (MDPI, 2025) Gencay, Burcu; Guler, Gunnur
    Understanding 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
    Magnetic Levitation-Based Determination of Single-Nuclei Density
    (Elsevier, 2026) Anil-Inevi, Muge; Sarigil, Oyku; Unal, Yagmur Ceren; Tekin, H. Cumhur; Mese, Gulistan; Ozcivici, Engin
    The 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
    Protection of N-Type (Ni,Fe)TiSb Half-Heusler Materials Against Static and Cyclic Oxidation Using a Si-Doped Cr Coating
    (Amer Chemical Soc, 2025) Gurtaran, Mikdat; Zhang, Zhenxue; Li, Xiaoying; Dong, Hanshan
    In this study, Cr-Si coatings were deposited on N-type (Ni,Fe)TiSb thermoelectric (TE) materials by using a closed-field unbalanced magnetron sputtering PVD technique. Oxidation behavior was evaluated under both isothermal (static) conditions (500 degrees C for 10 h and 600 degrees C for 50 h) and thermal cycling regimens (500 and 600 degrees C for 10 or 50 1 h cycles). Mass gain, surface morphology, cross-sectional microstructure, elemental distribution, and phase composition were examined by using scanning electron microscopy (SEM), energy-dispersive X-ray spectroscopy (EDX), and X-ray diffraction (XRD). Regardless of exposure mode, uncoated samples oxidized severely: a duplex scale formed, consisting of an outer TiO2 layer and a subjacent NiSb-rich zone, accompanied by extensive cracking and delamination. In sharp contrast, the Cr-Si coatings remained thermally stable and highly oxidation-resistant, maintaining the substrate's integrity during both static and cyclic tests. After exposure, coated samples showed negligible mass gain, no discernible morphological change, and no mechanical damage, confirming that the Cr-Si layer markedly enhances thermal durability and prevents surface degradation.
  • Article
    Beyond Traditional Dentistry: How Organoids and Next-Gen Hydrogels Are Redesigning Dental Tissue Regeneration
    (Elsevier, 2026) Yilmaz-Dagdeviren, Hilal Deniz; Arslan, Yavuz Emre
    Dental 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
    Comparative Proteomic Analysis of Dental-Origin Stem Cells: Insights Into Regenerative Potential
    (Springer, 2025) Tez, Banu Cicek; Durukan, Sebahat Melike; Yildir, Selin Kubra; Cokkececi, Murat; Boyvat, Dudu; Altinsoy, Nilay; Ozcan, Servet
    Teeth are a significant source of stem cells and have clinical importance for regenerative medicine. A human tooth harbors different kinds of stem cells in the dental pulp (DPSC) or the periodontal ligament (PDLSC). Also exfoliated teeth in childhood contain a special type of stem cells in their pulp called Stem cells from Human Exfoliated Deciduous teeth (SHED). All these stem cells have features and capacities that vary depending on their niche. Here we investigated the proteomic properties of three types of stem cells that originated from human teeth. We isolated and cultured the DPSCs, PDLSCs, and SHED cells. After validating MSC populations via immunophenotyping, we performed a mass spectrometry-based proteomic approach to identify and relatively quantify whole cell and secreted proteins. Identified proteins were evaluated by using Gene Ontology and Reactome pathway analysis tools. Our data reveal that SHED cells represented inflammation, hypoxia, and nutrient deficiency-associated ontologies in both their secretome and whole-cell proteomes. The whole-cell proteome of PDLSCs consisted of differentiation and proliferation-associated molecules while their secretory molecules were mainly associated with inflammation, ECM organization, and immune response. Among dental-originated stem cells, DPSCs appeared to be the healthiest and clinically relevant in terms of proteomic properties with their proliferation, growth factor signaling, and stemness-associated molecules in their secretome and whole-cell proteome. Obtained results demonstrated that every type of stem cell from dental origin has unique proteomic features that are altered by their location and physiological conditions. The findings may help researchers improve the dental stem-cell-based regenerative medicine approaches.
  • Article
    Effect of Marination on the Formation of Polycyclic Aromatic Hydrocarbons in Grilled Vegetables
    (Wiley, 2025) Kacmaz Ozcetin, Sibel; Artok, Levent
    The 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: 3
    Citation - Scopus: 4
    Evaluation of in Vivo and in Vitro Toxicity of Chestnut (Castanea Mollissima Blume) Plant: Developmental Toxicity in Zebrafish Embryos Cytotoxicity, Antioxidant Activity, and Phytochemical Composition by LC-ESI-MS/MS
    (John Wiley and Sons Inc, 2025) Demirtas, Ibrahim; Atalar, Mehmet Nuri; Bingol, Zeynebe; Kokturk, Mine; Ozhan, Gunes; Abdelsalam, Amine Hafis; Gulcin, Ilhami
    The search for novel therapeutic agents has led to increasing interest in natural products, driven by the recognition that they may offer safer and more sustainable alternatives to synthetic drugs. This study aims to fill the gap in knowledge regarding the biological activity and safety of the water extract of chestnut (Castanea mollissima) (chestnut), a plant species with a long history of use in traditional medicine, by conducting a comprehensive evaluation of its antioxidant, antidiabetic, and neuroprotective properties. This study presents a comprehensive analysis of the water extract of chestnut for the first time using various bioanalytical antioxidant methods. The extract's inhibitory effects on key enzymes like acetylcholinesterase (AChE), butyrylcholinesterase (BChE), and alpha-glycosidase were evaluated due to their relevance in metabolic and neurodegenerative disorders such as diabetes and Alzheimer's disease. Developmental toxicity and cytotoxicity were assessed using zebrafish (Danio rerio) embryos to evaluate the extract's biological safety. The major phenolic compounds present in the extract were identified by liquid chromatography-electrospray ionization tandem mass spectrometry (LC-ESI-MS/MS), revealing catechin, gallic acid, taxifolin, and epicatechin as the predominant constituents. Antioxidant capacity was determined through radical scavenging assays using 2,2-diphenyl-1-picrylhydrazyl (DPPH center dot) and 2,2 '-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS center dot+), alongside ferric (Fe3+), cupric (Cu2+), and Fe3+-TPTZ (ferric-tripyridyltriazine) reducing power assays. The findings highlight the significant antioxidant, antidiabetic, and neuroprotective potential of the chestnut water extract, supporting its prospective use in pharmaceutical and nutraceutical applications.
  • Article
    Citation - WoS: 5
    Citation - Scopus: 5
    Magnetically Controllable and Degradable Milliscale Swimmers as Intraocular Drug Implants
    (Wiley, 2025) Yildiz, E.; Bozuyuk, U.; Yildiz, E.; Wang, F.; Han, M.; Karacakol, A.C.; Sitti, M.
    Intraocular drug implants are increasingly used for retinal treatments, such as age-related macular degeneration and diabetic macular edema, due to the rapidly aging global population. Although these therapies show promise in arresting disease progression and improving vision, intraocular implant-based therapies can cause unexpected complications that require further surgery due to implant dislocation or uncontrolled drug release. These frequent complications of intraocular drug implants can be overcome using magnetically controllable degradable milliscale swimmers (MDMS) with a double-helix body morphology. A biodegradable hydrogel, polyethylene glycol diacrylate, is employed as the primary 3D printing material of MDMS, and it is magnetized by decorating it with biocompatible polydopamine-encapsulated iron-platinum nanoparticles. MDMS have comparable dimensions to commercial intraocular implants that achieve translational motions in both aqueous and vitreous bodies. They can be imaged in real-time using optical coherence tomography, ultrasound, and photoacoustic imaging. Thanks to their biodegradable hydrogel-based structure, they can be loaded with anti-inflammatory drug molecules and release the medications without disrupting retinal epithelial viability and barrier function, and decrease proinflammatory cytokine release significantly. These magnetically controllable swimmers, which degrade in a couple of months, can be used for less invasive and more precise intraocular drug delivery compared to commercial intraocular drug implants. © 2025 The Author(s). Advanced Science published by Wiley-VCH GmbH.