PubMed İndeksli Yayınlar Koleksiyonu / PubMed Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/11147/7645
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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: 1Improved Isolation of Ultra-High Genomic Dna Suitable for Third-Generation Sequencing(Mdpi, 2025) Ova, Ayse Oyku; Joffre, Enrique; Shafagh, Reza Zandi; Assuncao, Mariana F. G.; Sidorov, Roman Y.; Santos, Lilia M. A.; Romling, UteAlthough a variety of protocols to isolate high-molecular-weight genomic DNA exist, the isolation and preservation of ultra-high-molecular-weight genomic DNA of sufficient quality and length for error-free third-generation sequencing remains challenging. Inspired by the isolation of high-molecular-weight DNA in agarose plugs suitable to be separated by pulsed-field gel electrophoresis, we report the construction of an incubation chamber for DNA isolation. The chamber is flanked by semi-permeable polycarbonate membranes of variable pore size for the selective diffusion of compounds and components, which allows efficient cell lysis and the subsequent isolation of ultra-high-molecular-weight genomic DNA without shearing. The designed experimental approach is simple, but effective in isolating high-quality ultra-long genomic DNA that is suitable for third-generation sequencing by Oxford Nanopore Technology from challenging bacterial samples. We envisage that genomic DNA isolation using the incubation chamber, or variations thereof, will facilitate the regular sequencing of megabasepair-long DNA fragments, with a multitude of applications in microbiology, immunology, oncology, paleontology and forensic science.Article Citation - WoS: 4Citation - Scopus: 3Unveiling Bone and Dental Regeneration Potential of Quince Seed Mucilage-Nanohydroxyapatite Scaffolds in Rabbit Mandibles(Wiley, 2025) Genc, Cigdem Cetin; Yilmaz-Dagdeviren, Hilal Deniz; Deniz, Yesim; Derkus, Burak; Degirmenci, Alpin; Arslan, Yavuz EmreDonor-side morbidity of autografting for maxillofacial region defect regeneration has directed attention to bioengineered scaffolds. Composite scaffolds that mimic the bone extracellular matrix (ECM) are the potential candidates for defect reconstruction. Herein, a plant-based regenerative hydrogel, quince seed mucilage (QSM), was enriched with the nanohydroxyapatite (nHAp) particles to construct composite scaffolds (QSM/nHAp). The emerging scaffold is able to induce cellular spheroid formation and regenerate the critical-sized bilateral mandibular defects in rabbits. The macroscopic observations, histochemical (HC) and immunohistochemical (IHC) stainings, mu-computer tomography (CT) scanning, quantitative real time-polymerase chain reaction (qRT-PCR) analyses, and scanning electron microscopy (SEM) imaging revealed that all QSM/nHAp scaffolds were swelled with host blood, filled the whole cavity, and sustained cellular infiltration without adverse reactions. The gradual biodegradation profile of the scaffolds improved bone regeneration by releasing nHAp particles from the scaffold. Strikingly, co-development of dental and bone regeneration was observed for all QSM/nHAp groups beginning after day 21. Moreover, QSM/nHAp scaffolds induced expression (> 2-fold) of bone and dental-related gene and protein expressions at the grafted area and sustained a proper platform for maxillofacial remodeling. Therefore, we strongly believe that such biocompatible plant-based constructs, compared with conventional medical devices used in maxillofacial surgery, could support and induce simultaneous bone and dental regeneration due to the intrinsic dynamics of the material.Article Citation - WoS: 2Citation - Scopus: 3Magnetic Levitational Assembly of Differentiated Sh-Sy5y Cells for Aβ-Induced 3d Alzheimer's Disease Modeling and Curcumin Screening(Wiley-v C H verlag Gmbh, 2025) Bilginer-Kartal, Rumeysa; Arslan-Yildiz, AhuAlzheimer's disease is one of the prevalent neurodegenerative diseases and is characterized by amyloid beta aggregate (A beta) accumulation. This study reports an A beta 1-42 induced 3D Alzheimer's disease modeling utilizing differentiated SH-SY5Y spheroids, which is carried out by Magnetic levitation approach, and the neuroprotective effect of Curcumin is further investigated on this model. For this purpose, SH-SY5Y spheroids are differentiated using Retinoic acid-Brain-derived neurotrophic factor sequentially during 3D cell culture. Differentiated spheroids maintained high viability and exhibited significant neuronal characteristics, as evidenced by increasing beta-III tubulin and NeuN expressions. 3D Alzheimer's disease model formation and neurotoxicity of A beta 1-42 aggregates are investigated on un-/differentiated spheroids, resulting in 65% and 51% cell viability, respectively. Characterization of the 3D Alzheimer's disease model is done by immunostaining of Choline acetyltransferase to investigate cholinergic neuron activity loss, showing a 2.2 decrease in fluorescence intensity. Further, Curcumin treatment on the 3D Alzheimer's disease model resulted in augmenting cell viability, confirming neuroprotective effect of Curcumin on A beta 1-42 induced Alzheimer's disease model. This study highlighted the magnetic levitation-based fabrication of A beta 1-42-induced 3D Alzheimer's disease model successfully, offering a promising experimental platform for other neurodegenerative disease research and potential clinical applications.Article Citation - WoS: 5Citation - Scopus: 5Nanoarchitectonics Approach To Graphite/Starch-supported Bioelectrode for Enhanced Supercapacitor Performance(Elsevier, 2025) Goren, Aysegul Yagmur; Dincer, IbrahimThere has been an increasing interest in finding suitable materials for supercapacitor applications in response to the growing need for energy, to use alternative energy sources to fossil fuels in addition to energy storage. In this regard, bio-based carbon-loaded materials can be a promising option for high-performance supercapacitors because of their abundance, diversity, and reproducibility with waste management strategies. In this study, a new graphite-loaded bioelectrode is synthesized for supercapacitor application. The electrochemical performance of the synthesized electrode is tested at room temperature using the cyclic voltammetry method, and the capacity and energy density of the electrodes are evaluated. The electrochemical performance of 1 g of graphiteloaded bioelectrode was 3.5 mA/cm2, while the specific capacitance value was 355.6 F/g at a current density of 0.5 A/g. Furthermore, the bioelectrode provided significant cyclic stability with 93.5% in specific capacitance value after 5000 charge/discharge cycles at the current density of 0.5 A/g. Consequently, the synthesized bioelectrode can be a promising option for energy storage as a sustainable electrode due to its superior conductivity, stability, and low cost.Article Citation - WoS: 2Citation - Scopus: 2Combined Treatment of Ketogenic Diet and Propagermanium Reduces Neuroinflammation in Tay-Sachs Disease Mouse Model(Springer/Plenum Publishers, 2025) Inci, Orhan Kerim; Seyrantepe, VolkanTay-Sachs disease is a rare lysosomal storage disorder caused by beta-Hexosaminidase A enzyme deficiency causing abnormal GM2 ganglioside accumulation in the central nervous system. GM2 accumulation triggers chronic neuroinflammation due to neurodegeneration-based astrogliosis and macrophage activity with the increased expression level of Ccl2 in the cortex of a recently generated Tay-Sachs disease mouse model Hexa-/-Neu3-/-. Propagermanium blocks the neuroinflammatory response induced by Ccl2, which is highly expressed in astrocytes and microglia. The ketogenic diet has broad potential usage in neurological disorders, but the knowledge of the impact on Tay-Sach disease is limited. This study aimed to display the effect of combining the ketogenic diet and propagermanium treatment on chronic neuroinflammation in the Tay-Sachs disease mouse model. Hexa-/-Neu3-/- mice were placed into the following groups: (i) standard diet, (ii) ketogenic diet, (iii) standard diet with propagermanium, and (iv) ketogenic diet with propagermanium. RT-PCR and immunohistochemistry analyzed neuroinflammation markers. Behavioral analyses were also applied to assess phenotypic improvement. Notably, the expression levels of neuroinflammation-related genes were reduced in the cortex of 140-day-old Hexa-/-Neu3-/- mice compared to beta-Hexosaminidase A deficient mice (Hexa-/-) after combined treatment. Immunohistochemical analysis displayed correlated results with the RT-PCR. Our data suggest the potential to implement combined treatment to reduce chronic inflammation in Tay-Sachs and other lysosomal storage diseases.Article Long-Term Outcomes of Türkiye's First Population-Based Mammography Screening Program: a Decade of Breast Cancer Detection and Survival Analysis in Bahçeşehir(Bmc, 2025) Ozcinar, Beyza; Aribal, Erkin; Cabioglu, Neslihan; Gurdal, Sibel Ozkan; Varol, Gamze; Akyurt, Nuran; Ozmen, VahitBackgroundThe Bah & ccedil;e & scedil;ehir population-based mammography screening program (BMSP) is an example of T & uuml;rkiye's first population-based screening program. This study aims to reveal the successful implementation of population-based secreening program in one of the low- and middle-income countries, T & uuml;rkiye and long-term results of patients diagnosed with breast cancer during BMSP. MethodsThis study was conducted between 2009 and 2019, in the Bah & ccedil;e & scedil;ehir county of Istanbul. Women between the ages of 40 and 69 living in this region were invited every two years to undergo clinical breast examination (CBE) and mammography screening. All data was recorded in a dedicated software program. Women diagnosed with breast cancer were followed as a separate cohort. ResultsDuring the 10-year screening period, 8,825 women were screened and 146 (1.7%) breast cancers were detected. The median age at diagnosis for these patients was 52.9 years (40-69). The risk of breast cancer was 1.39 times higher (95% CI: 1.01-1.93) in women aged >= 50 compared to those less than 50 years (p = 0.045). The Cox regression analysis revealed that age at first birth, and number of births were significant predictors of breast cancer risk (p < 0.001, and p = 0.011). The breast cancer rate tends to increase as the breast density category progresses from A to D (p < 0.001). The median follow-up time for 146 breast cancer patients was 95.3 months. The 10-year breast cancer specific survival rate was 85%. ConclusionsThis study demonstrates that with a committed team and sufficient infrastructure, screening mammography can be effectively carried out in T & uuml;rkiye, leading to early detection and lower mortality rates. The recommended age to commence screening is 40 years old.Article Citation - WoS: 7Citation - Scopus: 7Comparative Analysis of Volume Change Behavior of Expansive Road Subgrades Stabilized With Waste Paper Sludge(Nature Portfolio, 2024) Tanyildizi, Muhammed; Goekalp, Islam; Zeybek, Abduelhakim; Uz, Volkan EmreExpansive soils have a high tendency for volume change in case of fluctuations in moisture content, potentially causing significant damage to light structures, particularly road pavements. This paper investigates the influence of waste paper sludge (\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\:WPS$$\end{document}) as an alternative sustainable stabilizer on the volume change behavior of expansive road subgrade soils of different origins. For this purpose, \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\:WPS$$\end{document} was added to the expansive soils at ratios of 3%, 6%, 9%, 12%, and 15% by dry weight of the soils. A series of Atterberg's limit, swelling, shrinkage, compaction, and consolidation tests were performed on pure soils and soil specimens with \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\:WPS$$\end{document} to attain a comprehensive understanding of the role that \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\:WPS$$\end{document} plays in the volume change behavior of expansive soils. The experimental test results showed that the addition of \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\:WPS\:$$\end{document} led to a considerable decrease in the plasticity and swell-shrink potentials of subgrade soils. The consolidation settlement of expansive road subgrades was also reduced to some extent with \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\:WPS$$\end{document}. Moreover, the statistical analysis of the test data indicated a significant relationship among different swelling-shrinkage parameters. The experimental results presented here suggest that the \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\:WPS$$\end{document} may be a cost-effective, environmentally friendly, and sustainable stabilizer to reduce the volume change sensitivity of expansive road subgrade soils.Article Citation - WoS: 2Citation - Scopus: 2Fabrication of Bioactive Helix Aspersa Extract-Loaded Chitosan-Based Bilayer Wound Dressings for Skin Tissue Regeneration(Amer Chemical Soc, 2024) Perpelek, Merve; Tıhmınlıoğlu, Funda; Tamburaci, Sedef; Karakasli, Ahmet; Tihminlioglu, FundaIn recent years, there has been a notable shift toward exploring plant and animal extracts for the fabrication of tissue engineering structures that seamlessly integrate with the human body, providing both biological compatibility and physical reinforcement. In this particular investigation, we synthesized bilayer wound dressings by incorporating snail (Helix aspersa) secretions, comprising mucus and slime, into chitosan matrices via lyophilization and electrospinning methodologies. A nanofiber layer was integrated on top of the porous structure to mimic the epidermal layer for keratinocyte activity as well as acting as an antibacterial barrier against possible infection, whereas a porous structure was designed to mimic the dermal microenvironment for fibroblast activity. Comprehensive assessments encompassing physical characterization, antimicrobial efficacy, in vitro bioactivity, and wound healing potential were conducted on these bilayer dressings. Our findings revealed that the mucus and slime extract loading significantly altered the morphology in terms of nanofiber diameter and average pore size. Snail extracts loaded on a nanofiber layer of bilayer dressings showed slight antimicrobial activity against Staphylococcus epidermidis and Escherichia coli. An in vitro release study of slime extract loaded in the nanofiber layer indicated that both groups 1 and 2 showed a burst release up to 6 h, and a sustained release was observed up to 96 h for group 1, whereas slime extract release from group 2 continued up to 72 h. In vitro bioactivity assays unveiled the favorable impact of mucus and slime extracts on NIH/3T3 fibroblast and HS2 keratinocyte cell attachment, proliferation, and glycosaminoglycan synthesis. Furthermore, our investigations utilizing the in vitro scratch assay showcased the proliferative and migratory effects of mucus and slime extracts on skin cells. Collectively, our results underscore the promising prospects of bioactive snail secretion-loaded chitosan constructs for facilitating skin regeneration and advancing wound healing therapies.Article Citation - WoS: 1Comparison of Cell-Penetrating and Fusogenic Tat-Ha2 Peptide Performance in Peptideplex, Multicomponent, and Conjugate Sirna Delivery Systems(Amer Chemical Soc, 2024) Uz, Metin; Bulmus, Volga; Altinkaya, Sacide AlsoyIn this study, the performance of the cell-penetrating and fusogenic peptide, TAT-HA2, which consists of a cell-permeable HIV trans-activator of transcription (TAT) protein transduction domain and a pH-responsive influenza A virus hemagglutinin protein (HA2) domain, was comparatively evaluated for the first time in peptideplex, multicomponent, and conjugate siRNA delivery systems. TAT-HA2 in all three systems protected siRNA from degradation, except in the conjugate system with a low Peptide/siRNA ratio. The synergistic effect of different peptide domains enhanced the transfection efficiency of multicomponent and conjugate systems compared to that of peptideplexes, which was attributed to the surface configuration of TAT-HA2 peptides depending on the nature of attachment. Particularly, the multicomponent system showed better cellular uptake and endosomal escape than the peptideplexes, resulting in enhanced siRNA delivery in the cytoplasm. In addition, the presence of cleavable disulfide bonds in multicomponent and conjugate systems promoted the effective siRNA delivery in the cytoplasm, resulting in improved gene silencing activity. The multicomponent system reduced the level of luciferase expression in SKOV3 cells to 45% (+/- 4). In contrast, the conjugate system and the commercially available siRNA transfection agent, Lipofectamine RNAiMax, caused luciferase suppression down to 55% (+/- 2) at a siRNA dose of 100 nM. For the same dose, the peptideplex system could only reduce the luciferase expression to 65% (+/- 5). None of the developed systems showed significant toxicity at any dose. Overall, the TAT-HA2 peptide is promising as a siRNA delivery vector; however, its performance depends on the nature of attachment and, as a result, its surface configuration on the developed delivery system.