PubMed İndeksli Yayınlar Koleksiyonu / PubMed Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/11147/7645
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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 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.Review Citation - WoS: 17Citation - Scopus: 16Engineering Periodontal Tissue Interfaces Using Multiphasic Scaffolds and Membranes for Guided Bone and Tissue Regeneration(Elsevier, 2024) Özkendir, Özge; Karaca, İlayda; Çullu, Selin; Yaşar, Hüsniye Nur,; Erdoğan, Oğulcan; Dikici, Serkan; Dikici, Betul AldemirPeriodontal diseases are one of the greatest healthcare burdens worldwide. The periodontal tissue compartment is an anatomical tissue interface formed from the periodontal ligament, gingiva, cementum, and bone. This multifaceted composition makes tissue engineering strategies challenging to develop due to the interface of hard and soft tissues requiring multiphase scaffolds to recreate the native tissue architecture. Multilayer constructs can better mimic tissue interfaces due to the individually tuneable layers. They have different characteristics in each layer, with modulation of mechanical properties, material type, porosity, pore size, morphology, degradation properties, and drug-releasing profile all possible. The greatest challenge of multilayer constructs is to mechanically integrate consecutive layers to avoid delamination, especially when using multiple manufacturing processes. Here, we review the development of multilayer scaffolds that aim to recapitulate native periodontal tissue interfaces in terms of physical, chemical, and biological characteristics. Important properties of multiphasic biodegradable scaffolds are highlighted and summarised, with design requirements, biomaterials, and fabrication methods, as well as post-treatment and drug/growth factor incorporation discussed.Article Citation - WoS: 1Citation - Scopus: 1Hdac9/P300 Immunoexpression and Migration Analysis for Malignant Melanoma Stem Cell(Elsevier, 2023) Özdil, Berrin; Asker Abdikan, Cemile Sinem; Özdemir, Merve; Erişik, Derya; Yesin, Taha Kadir; Avcı, Çığır Biray; Kurkutçu, Yeşim; Güler, Günnur; Aktuğ, HüseyinMelanoma is an aggressive tumor with a poor prognosis that worsens in the metastatic phase. Distruptions of epigenetic mechanisms is known to effect cancer stem cells (CSCs) activity. Malignant melanoma (MM) progression may be promoted by changes in the genetic structure of CSC. Thus, treatments that target epigenetic modifications could be a promising weapon, especially in melanoma. Here, we compared p300, HDAC9, and Factin proteins in melanoma CSCs (CD133+), non-CSCs (CD133-) and CHL-1 cell line, as well as cell migration and division rates. At 4 and 6 h, P300 protein levels in CHL-1 and CD133 + were remarkably similar, and the CD133- showed increases in expression levels as the incubation period lengthened. HDAC9 protein intensity decreased in CHL-1, increased in the CD133-, and remained relatively unchanged in the CD133+ as the incubation period lengthened. The mean value of F-actin expression level increased in all cell group with time, when the highest increase observed in CHL-1. In conclusion, our studies contribute to the management of metastatic diseases in the future and offer new insight into the molecular basis of the initiation and progression of MM.Letter Citation - WoS: 1Citation - Scopus: 2C-Met Activation Promotes Extravasation of Hepatocellular Carcinoma Cells Into 3d-Cultured Hepatocyte Cells in Lab-On Device(Elsevier, 2023) Solmaz, Gülhas; Bağcı, Gülsün; Çömez, Dehan; Topel, Hande; Yılmaz, Yeliz; Bağırsakçı, Ezgi; Güneş, Aysim; Batı Ayaz, Gizem; Tahmaz, İsmail; Bilgen, Müge; Pesen Okvur, DevrimActivation of c-Met signaling is associated with an aggressive phenotype and poor prognosis in hepatocellular carcinoma (HCC); however, its contribution to organ preference in metastasis remains unclear. In this study, using a Lab on a Chip device, we defined the role of aberrant c-Met activation in regulating the extravasation and homing capacity of HCC cells. Our studies showed that (i) c-Met overexpression and activation direct HCC cells preferentially towards the hepatocytes-enriched microenvironment, and (ii) blockage of c-Met phosphorylation by a small molecule inhibitor attenuated extravasation and homing capacity of HCC cells. These results, thus, demonstrate the role of c-Met signaling in regulating the colonization of HCC cells preferentially in the liver. © 2023 Elsevier B.V.Article Citation - WoS: 4Citation - Scopus: 4Mitigation Potential of Zingerone and Rutin on Toxicity Mechanisms of Nickel To Zebrafish Based on Morphological, Dna Damage and Apoptosis Outcome Analysis(Elsevier, 2023) Köktürk, Mine; Yıldırım, Serkan; Atamanalp, Muhammed; Kılıçoğlu, Metin; Uçar, Arzu; Özhan, Güneş; Alak, GoncaAlthough nickel (Ni) is an important cofactor for various enzymes in biological systems, it can cause serious problems when insufficient or excessive in an organism. Therefore, it is very important to investigate Ni in biological systems, especially in cells with its related pathogenic mechanism. This study was carried out to demonstrate the effects of zingerone (ZO) and rutin (RN) administration against nickel chloride (NiCl2) toxicity on neurobehavioral performance and brain oxidative status in zebrafish (Danio rerio) embryos/larvae on histological perspective. The experimental design of the study, which included twenty groups of fish, each containing 10 embryos, was prepared as semi-static and the trial continued for 96 hpf. In the obtained findings, it was determined that ZO and RN had a mitigating effect in this toxicity table where Ni caused oxidative stress in zebrafish larvae, induced DNA damage and apoptosis. A similar picture is valid for malformation processes as well as survival and hatching rates. These results showed that nickel is toxic to developing embryos via acting different mechanisms. In conclusion, we observed that ZO and RN have a greater effect on physiology, DNA damage and apoptosis than gross morphology, with a significant ameliorative effect.Article Citation - WoS: 4Citation - Scopus: 3Boron Stress Signal Is Transmitted Through the Tor Pathway(Elsevier, 2023) Uluışık, İrem; Koç, AhmetAlthough boron is an essential element for many organisms, an excess amount of it can cause toxicity, and the mechanism behind this toxicity is not yet fully understood. The Gcn4 transcription factor plays a crucial role in the boron stress response by directly activating the expression of the boron efflux pump Atr1. More than a dozen transcription factors and multiple cell signaling pathways have roles in regulating the Gcn4 transcription factor under various circumstances. However, it is unknown which pathways or factors mediate boron signaling to Gcn4. Using the yeast Saccharomyces cerevisiae as a model, we analyzed the factors that converge on the Gcn4 transcription factor to assess their possible roles in boron stress signaling. Our findings show that the GCN system is activated by uncharged tRNA stress in response to boron treatment and that GCN1, which plays a role in transferring uncharged tRNAs to Gcn2, is necessary for the kinase activity of Gcn2. The SNF and PKA pathways were not involved in mediating boron stress, even though they interact with Gcn4. Mutations in TOR pathway genes, such as GLN3 and TOR1, abolished Gcn4 and ATR1 activation in response to boric acid treatment. Therefore, our study suggests that the TOR pathway must be functional to form a proper response against boric acid stress.Article Citation - WoS: 9Citation - Scopus: 8Quantitative Determination of Phenolic Compounds in Propolis Samples From the Black Sea Region (türkiye) Based on Hptlc Images Using Partial Least Squares and Genetic Inverse Least Squares Methods(Elsevier, 2023) Güzelmeriç, Etil; Özdemir, Durmuş; Şen, Nisa Beril; Çelik, Cansel; Yeşilada, ErdemThe complex chemical composition of propolis is related to the plant source to be used by honeybees. Propolis type is defined based on the plant source with the highest proportion in its composition, which is determined by chromatographic techniques as high-performance thin-layer chromatography (HPTLC). In addition to marker component identification to specify the propolis type, quantification of its proportion is also significant for prediction and reproducible pharmacological activity. One drawback for propolis marker component quantita-tion is that during the chromatographical analysis, not the main but the other plant sources with less proportion may cause interferences during the chemical analysis. In this study, the amounts of marker components were compared with the reference analysis data obtained by high-performance liquid chromatography (HPLC) and from HPTLC images using Partial Least Squares (PLS) and Genetic Inverse Least Squares (GILS) regression methods. Firstly, HPTLC images of propolis samples were processed by an image algorithm (developed in MATLAB) where the bands of each standard and the samples were cut same dimensional pieces as 351 x 26 pixels in height and width, respectively. Simultaneously, reference analysis of the marker components in propolis samples was performed with a validated HPLC method. Consequently, the reference values obtained from HPLC versus PLS, and GILS predicted values of the eight compounds based on the digitized HPTLC images of the chromatograms were found to be matched successfully. The results of the multivariate calibration models demonstrated that HPTLC images could be used quantitatively for quality control of propolis used as a food supplement.Article Citation - WoS: 3Citation - Scopus: 3Quasi-Static and Dynamic Brazilian Testing and Failure Analysis of a Deer Antler in the Transverse To the Osteon Growth Direction(Elsevier, 2023) Orhan, Mehmet; Sarıkaya, Mustafa Kemal; Taşdemirci, Alper; Tuncer, Can; Güden, MustafaThe transverse tensile strength of a naturally fallen red deer antler (Cervus Elaphus) was determined through indirect Brazilian tests using dry disc-shape specimens at quasi-static and high strain rates. Dynamic Brazilian tests were performed in a compression Split-Hopkinson Pressure Bar. Quasi-static tensile and indirect Brazilian tests were also performed along the osteon growth direction for comparison. The quasi-static transverse tensile strength ranged 31.5–44.5 MPa. The strength increased to 83 MPa on the average in the dynamic Brazilian tests, proving a rate sensitive transverse strength. The quasi-static tensile strength in the osteon growth direction was however found comparably higher, 192 MPa. A Weibull analysis indicated a higher tensile ductility in the osteon growth direction than in the transverse to the osteon growth direction. The microscopic analysis of the quasi-static Brazilian test specimens (tensile strain along the osteon growth direction) revealed a micro-cracking mechanism operating by the crack deflection/twisting at the lacunae in the concentric lamellae region and at the interface between concentric lamellae and interstitial lamellae. On the other side, the specimens in the transverse direction fractured in a more brittle manner by the separation/delamination of the concentric lamellae and pulling of the interstitial lamellae. The detected increase in the transverse strength in the high strain rate tests was further ascribed to the pull and fracture of the visco-plastic collagen fibers in the interstitial lamellae. This was also confirmed microscopically; the dynamically tested specimens exhibited flatter fracture surfaces. © 2023 Elsevier LtdArticle Citation - WoS: 4Citation - Scopus: 4Mobile human ad hoc networks: A communication engineering viewpoint on interhuman airborne pathogen transmission(Elsevier, 2022) Güleç, Fatih; Atakan, Barış; Dressler, FalkoA number of transmission models for airborne pathogens transmission, as required to understand airborne infectious diseases such as COVID-19, have been proposed independently from each other, at different scales, and by researchers from various disciplines. We propose a communication engineering approach that blends different disciplines such as epidemiology, biology, medicine, and fluid dynamics. The aim is to present a unified framework using communication engineering, and to highlight future research directions for modeling the spread of infectious diseases through airborne transmission. We introduce the concept of mobile human ad hoc networks (MoHANETs), which exploits the similarity of airborne transmission-driven human groups with mobile ad hoc networks and uses molecular communication as the enabling paradigm. In the MoHANET architecture, a layered structure is employed where the infectious human emitting pathogen-laden droplets and the exposed human to these droplets are considered as the transmitter and receiver, respectively. Our proof-of-concept results, which we validated using empirical COVID-19 data, clearly demonstrate the ability of our MoHANET architecture to predict the dynamics of infectious diseases by considering the propagation of pathogen-laden droplets, their reception and mobility of humans.