PubMed İndeksli Yayınlar Koleksiyonu / PubMed Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/11147/7645
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Article Citation - WoS: 5Citation - Scopus: 5Differences and Similarities in Biophysical and Biological Characteristics Between U87 Mg Glioblastoma and Astrocyte Cells(Springer, 2023) Özdil, Berrin; Çalık Kocatürk, Duygu; Altunayar Ünsalan, Çisem; Açıkgöz, Eda; Oltulu, Fatih; Görgülü, Volkan; Uysal, Ayşegül; Öktem, Gülperi; Ünsalan, Ozan; Güler, Günnur; Aktuğ, HüseyinCurrent cancer studies focus on molecular-targeting diagnostics and interactions with surroundings; however, there are still gaps in characterization based on topological differences and elemental composition. Glioblastoma (GBM cells; GBMCs) is an astrocytic aggressive brain tumor. At the molecular level, GBMCs and astrocytes may differ, and cell elemental/topological analysis is critical for identifying potential new cancer targets. Here, we used U87 MG cells for GBMCS. U87 MG cell lines, which are frequently used in glioblastoma research, are an important tool for studying the various features and underlying mechanisms of this aggressive brain tumor. For the first time, atomic force microscopy (AFM), scanning electron microscopy (SEM) accompanied by energy-dispersive X-ray spectroscopy (EDS), and X-ray photoelectron spectroscopy (XPS) are used to report the topology and chemistry of cancer (U87 MG) and healthy (SVG p12) cells. In addition, F-actin staining and cytoskeleton-based gene expression analyses were performed. The degree of gene expression for genes related to the cytoskeleton was similar; however, the intensity of F-actin, anisotropy values, and invasion-related genes were different. Morphologically, GBMCs were longer and narrower while astrocytes were shorter and more disseminated based on AFM. Furthermore, the roughness values of these cells differed slightly between the two call types. In contrast to the rougher astrocyte surfaces in the lamellipodial area, SEM-EDS analysis showed that elongated GBMCs displayed filopodial protrusions. Our investigation provides considerable further insight into rapid cancer cell characterization in terms of a combinatorial spectroscopic and microscopic approach.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.Article Citation - WoS: 11Citation - Scopus: 13Proteolysis of Micellar Β-Casein by Trypsin: Secondary Structure Characterization and Kinetic Modeling at Different Enzyme Concentrations(MDPI, 2023) Vorob’ev, Mikhail M.; Açıkgöz, Burçin Dersu; Güler, Günnur; Golovanov, Andrey V.; Sinitsyna, Olga V.Tryptic proteolysis of protein micelles was studied using β-casein (β-CN) as an example. Hydrolysis of specific peptide bonds in β-CN leads to the degradation and rearrangement of the original micelles and the formation of new nanoparticles from their fragments. Samples of these nanoparticles dried on a mica surface were characterized by atomic force microscopy (AFM) when the proteolytic reaction had been stopped by tryptic inhibitor or by heating. The changes in the content of β-sheets, α-helices, and hydrolysis products during proteolysis were estimated by using Fourier-transform infrared (FTIR) spectroscopy. In the current study, a simple kinetic model with three successive stages is proposed to predict the rearrangement of nanoparticles and the formation of proteolysis products, as well as changes in the secondary structure during proteolysis at various enzyme concentrations. The model determines for which steps the rate constants are proportional to the enzyme concentration, and in which intermediate nano-components the protein secondary structure is retained and in which it is reduced. The model predictions were in agreement with the FTIR results for tryptic hydrolysis of β-CN at different concentrations of the enzyme.Article Citation - WoS: 11Citation - Scopus: 10Intercalation Leads To Inverse Layer Dependence of Friction on Chemically Doped Mos2(IOP Publishing, 2023) Açıkgöz, Oğulcan; Guerrero, Enrique; Yanılmaz, Alper; Dağdeviren, Ömür E.; Çelebi, Cem; Strubbe, David A.; Baykara, Mehmet Z.We present results of atomic-force-microscopy-based friction measurements on Re-doped molybdenum disulfide (MoS2). In stark contrast to the widespread observation of decreasing friction with increasing number of layers on two-dimensional (2D) materials, friction on Re-doped MoS2 exhibits an anomalous, i.e. inverse, dependence on the number of layers. Raman spectroscopy measurements combined with ab initio calculations reveal signatures of Re intercalation. Calculations suggest an increase in out-of-plane stiffness that inversely correlates with the number of layers as the physical mechanism behind this remarkable observation, revealing a distinctive regime of puckering for 2D materials.Article Citation - WoS: 2Citation - Scopus: 2Highly Mobile Excitons in Single Crystal Methylammonium Lead Tribromide Perovskite Microribbons(American Chemical Society, 2022) McClintock, Luke; Song, Ziyi; Travaglini, H. Clark; Senger, Ramazan Tuğrul; Chandrasekaran, Vigneshwaran; Htoon, Han; Yarotski, Dmitry; Yu, DongExcitons are often given negative connotation in solar energy harvesting in part due to their presumed short diffusion lengths. We investigate exciton transport in single-crystal methylammonium lead tribromide (MAPbBr3) microribbons via spectrally, spatially, and temporally resolved photocurrent and photoluminescence measurements. Distinct peaks in the photocurrent spectra unambiguously confirm exciton formation and allow for accurate extraction of the low temperature exciton binding energy (39 meV). Photocurrent decays within a few μm at room temperature, while a gate-tunable long-range photocurrent component appears at lower temperatures (about 100 μm below 140 K). Carrier lifetimes of 1.2 μs or shorter exclude the possibility of the long decay length arising from slow trapped-carrier hopping. Free carrier diffusion is also an unlikely source of the highly nonlocal photocurrent, due to their small fraction at low temperatures. We attribute the long-distance transport to high-mobility excitons, which may open up new opportunities for novel exciton-based photovoltaic applications.Article Citation - WoS: 2Citation - Scopus: 3Transport Modeling of Locally Photogenerated Excitons in Halide Perovskites(American Chemical Society, 2021) Tang, Kuen Wai; Li, Senlei; Weeden, Spencer; Song, Ziyi; McClintock, Luke; Xiao, Rui; Senger, Ramazan TuğrulExcitons have fundamental impacts on optoelectronic properties of semiconductors. Halide perovskites, with long carrier lifetimes and ionic crystal structures, may support highly mobile excitons because the dipolar nature of excitons suppresses phonon scattering. Inspired by recent experimental progress, we perform device modeling to rigorously analyze exciton formation and transport in methylammonium lead triiodide under local photoexcitation by using a finite element method. Mobile excitons, coexisting with free carriers, can dominate photocurrent generation at low temperatures. The simulation results are in excellent agreement with the experimentally observed strong temperature and gate dependence of carrier diffusion. This work signifies that efficient exciton transport can substantially influence charge transport in the family of perovskite materials.Article Citation - WoS: 5Citation - Scopus: 6Tuning the Structural, Electronic and Dynamical Properties of Janus M4x3y3 (m = Pd, Ni and Co; X,y = S, Se and Te) Monolayers: a Dft Study(Royal Society of Chemistry, 2021) Eren, İsmail; Akgenç, BernaBased on density functional theory, the structural, electronic and vibrational properties of two-dimensional transition metal chalcogenides M2X3 and their Janus type M4X3Y3, where M = Pd, Co and Ni and X = Se, S and Te, are investigated. Motivated by the successful synthesis of a 2D Pd2Se3 monolayer and the proof of the dynamical stability of Ni2Se3 and Co2Se3 monolayers, in terms of the phonon band dispersions, we have systemically studied the fundamental physical properties of Janus transition metal chalcogenides, such as their structural, phonon and thermodynamic stability and their electronic and mechanical properties. Our results show that Janus structures of M4X3Y3 are energetically favorable and dynamically stable. The ab initio molecular dynamic simulations (AIMD) results clearly prove that they kept their thermal stability at room temperature. We have demonstrated their structural, electronic and vibrational properties and Raman spectra. The electronic band dispersions show that monolayer Co2Se3 shows half-metal properties with a moderate band gap (1.01 eV), Pd2Se3 has a 1.42 eV direct band gap, while Ni2Se3 has a 1.38 eV indirect band gap. Pd4Se3S3, Pd4Se3Te3 and Pd4S3Te3 are indirect band gap semiconductors with band gaps of 1.22 eV, 1.05 eV and 0.61 eV, respectively. Ni4Se3S3, Ni4Se3Te3 and Ni4S3Te3 are indirect band gap semiconductors with band gaps of 1.61 eV, 0.77 eV and 0.49 eV, respectively. While pristine Co2Se3 is shown to have half-metallicity (HM), the HM behaviour of the Janus Co4Se3Te3 and Co4S3Te3 monolayers disappear and Co4Se3S3 remains a HM with a moderate band gap of 0.85 eV. In addition, the Raman spectra of these Janus materials are shown to exhibit totally distinctive features as compared to those of the pristine materials. This work reveals the important material properties of Janus type M4X3Y3 monolayers, where M = Pd, Co and Ni and X = Se, S and Te, which could have wide applications in new functional devices.Article Citation - WoS: 3Citation - Scopus: 3Compact Multilayer Thin-Film Color Filters and Direct Integration on White-Light Diodes for Color Conversion(Optical Society of America, 2021) Yiğen, Serap; Ekmekçioğlu, Merve; Özdemir, Mehtap; Aygün, Gülnur; Özyüzer, LütfiWe present highly efficient green, yellow, and red filters based on a metal-dielectric structure. The filters encompass only five layers of alternating zinc tin oxide and silver thin films that are grown on soda lime glass and white light-emitting diodes (LEDs) using direct current magnetron sputtering at room temperature. The designed filters provide efficient color filtering in the visible spectrum. High purity colored light is obtained by direct application of filters on LEDs as color converters. The presented method offers an easy way for realizing different colors by tuning the thicknesses of layers in the structure. (C) 2021 Optical Society of AmericaArticle Citation - WoS: 11Citation - Scopus: 13Effect of Cnt Incorporation on Pan/Ppy Nanofibers Synthesized by Electrospinning Method(TÜBİTAK, 2020) İnce Yardımcı, Atike; Tanoğlu, Metin; Yılmaz, Selahattin; Selamet, YusufIn this study, carbon nanotubes (CNTs) added polyacrylonitrile/polypyrrole (PAN/PPy) electrospun nanofibers were produced. Average diameters of the nanofibers were measured as 268 and 153 nm for 10 and 25 wt% of PPy contents, respectively. A relatively higher strain to failure values (23.3%) were observed for the low PPy content. When as-grown CNTs (1 and 4 wt%) were added into the PAN/PPy blends, disordered nanofibers were observed to form within the microstructure. To improve the interfacial properties of CNTs/PAN/PPy composites, CNTs were functionalized with H2SO4/HNO3/HCl solution. The functionalized CNTs were well dispersed within the nanofibers and aligned along the direction of nanofibers. Therefore, beads formation on nanofibers decreased. The impedance of the nanofibers was found to decrease with the PPy content and CNT addition. These nanofibers had a great potential to be used as an electrochemical actuator or a tissue engineering scaffold.Article Citation - WoS: 24Citation - Scopus: 24Defect Tolerant and Dimension Dependent Ferromagnetism in Mnse2(Royal Society of Chemistry, 2019) Eren, İsmail; İyikanat, Fadıl; Şahin, HasanBy performing density functional theory-based calculations, we investigate the structural, vibrational, electronic and magnetic properties of 2D monolayers, nanoribbons and quantum dots of MnSe2. Vibrational spectrum analysis reveals the dynamical stability of not only ferromagnetic but also antiferromagnetic phases of single layer MnSe2 crystal structures. Electronically, calculations show that 1T-MnSe2 is a ferromagnetic structure displaying metallic behavior. It is also found that the structure preserves its dynamical stability and metallic behavior even under the presence of high density Se vacancies. Moreover, it was predicted that, differing from the 2D MnSe2, metal-metal interaction driven reconstructions result in ferromagnetic-to-antiferromagnetic crossover in the ground state of nanoribbons and quantum dots. With its robust ferromagnetic metallic character in the 2D ultra-thin limit and dimension-dependent magnetic properties, MnSe2 is an important candidate for spintronic device applications.