PubMed İndeksli Yayınlar Koleksiyonu / PubMed Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/11147/7645
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Article Development of Self-Assembled Peptide Hydrogels Containing Matrix-Metalloproteinase Degradable Motifs for 3D Lung Cancer Models(Royal Society of Chemistry, 2026) Top, Ayben; Sırma Tarım, Burcu; Top, Ayben; 03.02. Department of Chemical Engineering; 03. Faculty of Engineering; 01. Izmir Institute of TechnologyHydrogel-forming peptides, including matrix metalloproteinase (MMP)-degradable motifs, have been employed to investigate cell-extracellular matrix interactions in vitro. However, their potential in 3D cancer models has been explored only in a few studies. In this study, we used modified MMP-2 degradable motifs (VSLRA or ASLRA) in the design of EDP1 (RVSLRADARVSLRADA) and EDP2 (RASLRADARASLRADA) peptide hydrogelators. The peptides self-assembled into nanofibrillar hydrogels with storage moduli between similar to 300 and similar to 400 Pa. MMP-2 degradation properties of the peptides were confirmed, and a slightly higher MMP-2 responsiveness of the EDP1 hydrogel was observed. The hydrogels were used in the encapsulation of A549 lung adenocarcinoma cancer cells and MRC-5 human lung fibroblast cells. The designed hydrogels supported the proliferation of these cells with high viability and induced cluster formation of encapsulated A549 cells similar to that observed with the RADA hydrogel. However, the hydrogel network structure affected the morphology of the migrated cells in the absence of curcumin. The addition of curcumin decreased the migration and invasion of A549 cells, resulting in a round cell morphology independent of the hydrogel matrices. Anticancer drug tests indicated that cell viability after drug treatment was higher in the 3D hydrogels than in 2D cultures. It was also confirmed that the combinational therapy of doxorubicin and curcumin decreased the cell proliferation and colonization to a greater extent compared to doxorubicin monotherapy. Thus, the hydrogels developed in this study can be used for 3D cancer models or other tissue engineering applications as an alternative to the RADA hydrogel by exploiting the MMP-2 degradation properties.Article Citation - Scopus: 7High-Pressure Structural Studies and Pressure-Induced Sensitisation of 3,4,5-Trinitro(Royal Society of Chemistry, 2023) Atceken, N.; Hemingway, J.; Bull, C.L.; Liu, X.; Michalchuk, A.A.L.; Konar, S.; Morrison, C.A.; 01. Izmir Institute of TechnologyHerein we report the first high-pressure study of the energetic material 3,4,5-trinitro-1H-pyrazole (3,4,5-TNP) using neutron powder diffraction and single-crystal X-ray diffraction. A new high-pressure phase, termed Form II, was first identified through a substantial change in the neutron powder diffraction patterns recorded over the range 4.6-5.3 GPa, and was characterised further by compression of a single crystal to 5.3 GPa in a diamond-anvil cell using X-ray diffraction. 3,4,5-TNP was found to be sensitive to initiation under pressure, as demonstrated by its unexpected and violent decomposition at elevated pressures in successive powder diffraction experiments. Initiation coincided with the sluggish phase transition from Form I to Form II. Using a vibrational up-pumping model, its increased sensitivity under pressure can be explained by pressure-induced mode hardening. These findings have potential implications for the safe handling of 3,4,5-TNP, on the basis that shock- or pressure-loading may lead to significantly increased sensitivity to initiation. © 2023 The Royal Society of Chemistry.Article Citation - WoS: 8Citation - Scopus: 9Development of Plant-Based Biopolymer Coatings for 3d Cell Culture: Boron-Silica Quince Seed Mucilage Nanocomposites(Royal Society of Chemistry, 2023) Yılmaz, Hilal Deniz; Cengiz, Uğur; Derkuş, Burak; Arslan, Yavuz Emre; 01. Izmir Institute of TechnologySpheroid formation with spontaneous aggregation has captured interest in most cell culture studies due to its easy set-up and more reliable results. However, the economic and technical costs of the advanced systems and commercial ultra-low adhesive platforms have pushed researchers into pursuing alternatives. Nowadays, polymeric coatings, including poly-hydroxyethyl methacrylate and agar/agarose, are the commonly used polymers for non-adhesive plate fabrication, yet the costs and working solvent or heat-dependent preparation procedures maintain the need for the development of novel biomaterials. Here, we propose a greener and more economical approach for producing non-adherent surfaces and spheroid formation. For this, a plant waste-based biopolymer from quince fruit (Cydonia oblonga Miller, from Rosaceae family) seeds and boron-silica precursors were introduced. The unique water-holding capacity of quince seed mucilage (Q) was enriched with silanol and borate groups to form bioactive and hydrophilic nanocomposite overlays for spheroid studies. Moreover, 3D gel plates from the nanocomposite material were fabricated and tested in vitro as a proof-of-concept. The surface properties of coatings and the biochemical and mechanical properties of the nanocomposite materials were evaluated in-depth with techniques, and extra hydrophilic coatings were obtained. Three different cell lines were cultured on these nanocomposite surfaces, and spheroid formation with increased cellular viability was recorded on day 3 with a >200 & mu;m spheroid size. Overall, Q-based nanocomposites are believed to be a fantastic alternative for non-adherent surface fabrication due to their low-cost, easy operation, and intrinsic hydration layer forming capacity with biocompatible nature in vitro.Article Citation - WoS: 16Citation - Scopus: 15Ultrasound-Assisted Dopamine Polymerization: Rapid and Oxidizing Agent-Free Polydopamine Coatings on Membrane Surfaces(Royal Society of Chemistry, 2021) Cihanoğlu, Aydın; Schiffman, Jessica D.; Alsoy Altınkaya, Sacide; 03.02. Department of Chemical Engineering; 03. Faculty of Engineering; 01. Izmir Institute of TechnologyHerein, we report a controllable pathway to accelerate the polymerization kinetics of dopamine using ultrasound as a trigger. The use of ultrasound was demonstrated to dramatically accelerate the slow liquid phase reaction kinetics and increase the deposition rate of the polydopamine coating on the surface of polymeric membranes.Article Citation - WoS: 2Citation - Scopus: 2Ultra-Thin Structures of Manganese Fluorides: Conversion From Manganese Dichalcogenides by Fluorination(Royal Society of Chemistry, 2021) Şahin, Hasan; Nair, Rahul R.; Peeters, François M.; Şahin, Hasan; 04.04. Department of Photonics; 04. Faculty of Science; 01. Izmir Institute of TechnologyIn this study, it is predicted by density functional theory calculations that graphene-like novel ultra-thin phases of manganese fluoride crystals, that have nonlayered structures in their bulk form, can be stabilized by fluorination of manganese dichalcogenide crystals. First, it is shown that substitution of fluorine atoms with chalcogens in the manganese dichalcogenide host lattice is favorable. Among possible crystal formations, three stable ultra-thin structures of manganese fluoride, 1H-MnF2, 1T-MnF2 and MnF3, are found to be stable by total energy optimization calculations. In addition, phonon calculations and Raman activity analysis reveal that predicted novel single-layers are dynamically stable crystal structures displaying distinctive characteristic peaks in their vibrational spectrum enabling experimental determination of the corresponding phases. Differing from 1H-MnF2 antiferromagnetic (AFM) large gap semiconductor, 1T-MnF2 and MnF3 single-layers are semiconductors with ferromagnetic (FM) ground state.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; Eren, İsmail; Akgenç, Berna; 04.05. Department of Pyhsics; 04. Faculty of Science; 01. Izmir Institute of TechnologyBased 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: 2Citation - Scopus: 2Palladium-Catalysed Regio- and Stereoselective Arylative Substitution of Gamma,delta-Epoxy Esters and Amides by Sodium Tetraaryl Borates(Royal Society of Chemistry, 2020) Bilgi, Yasemin; Kuş, Melih; Kuş, Melih; Artok, Levent; Artok, Levent; 04.01. Department of Chemistry; 04. Faculty of Science; 01. Izmir Institute of TechnologyPalladium-catalysed reactions of gamma,delta-epoxy-alpha,beta-unsaturated esters and amides with NaBAr(4)reagents proceeded regio- and stereoselectively, producing allylic homoallyl alcohols with aryl-substituents in the allylic position for a wide range of substrates. AsPh(3)was found to be a competent ligand for the arylation reaction, whereas phosphine ligand/Lewis acidic organoboron combinations favoured the substitution reaction by oxygen nucleophiles (e.g.H2O, ROH).Article Citation - WoS: 16Citation - Scopus: 20Smartphone-Assisted Hepatitis C Detection Assay Based on Magnetic Levitation(Royal Society of Chemistry, 2020) Özefe, Fatih; Arslan Yıldız, Ahu; Yıldız, Ahu Arslan; Özefe, Fatih; 01. Izmir Institute of Technology; 03.01. Department of Bioengineering; 03. Faculty of EngineeringThis work describes development of smartphone-assisted magnetic levitation assay forPoint-of-Care(PoC) applications. Magnetic levitation is a technique that detects and separates particles based on their density differences in a magnetic field. Observation of the levitated micro-particles is mainly performed by light microscope or additional optical components, which mostly limits applicability of the magnetic levitation technique for PoC diagnostics. In this paper, we demonstrated the capability of the smartphone assisted-magnetic levitation platform for Hepatitis C (HCV) detection assay. This method utilizes microsensor beads (MS beads) that are functionalized with anti-HCV NS3 antibody. First, the magnetic levitation platform was optimizedviadensity marker polyethylene beads (DMB); then HCV NS3 protein was successfully detected based on levitation height differences of MS beads caused by density changes. The capability of the magnetic levitation platform for HCV detection was determined as almost 10-fold sensitive compared to conventional techniques such as enzyme-linked immunosorbent assay (ELISA). The imaging capability and resolution of the setup was improved over previously used configurations, and the developed platform enabled visualization of micro-scale objects only by smartphone assistance. This method requires no power, it is an easy-to-use and cost effective, therefore it could be easily adaptable to varied sensing assays as PoC tool.Article Citation - WoS: 26Citation - Scopus: 27Electric Charge of Nanopatterned Silica Surfaces(Royal Society of Chemistry, 2019) Özçelik, H. Gökberk; Barışık, Murat; Barışık, Murat; 03.10. Department of Mechanical Engineering; 03. Faculty of Engineering; 01. Izmir Institute of TechnologyThe most recent technologies employ nanoscale surface patterning or roughening in order to engineer desired properties on a surface. Electrokinetic properties at the interface of such surfaces and ionic liquids show different behavior to the well-known theoretical descriptions. Basically, the ionic distribution on the surface differs due to electrical double layer overlap effects in the pits and curvature effects at the tips of surface structures. Generally, the charge density of a surface is assumed to be a material property and surface roughness effects are overlooked in most of the literature. In contrast, we properly calculated the local surface charges based on surface chemistry at the corresponding local ionic concentration (charge regulation) for various surface roughness and solution conditions. The results showed that the surface charge density of silica decreased at the pits but increased at the tips of surface patterns. Even for the simplest case of self-repeating surface structures, the average of local surface charges becomes lower than the theoretical predictions. Based on numerical calculations, a phenomenological model was developed as an extension to the existing flat surface theory, which can successfully predict the average surface charge on a nano patterned surface as a function of the surface pattern size, ionic concentration and pH.Article Citation - WoS: 22Citation - Scopus: 22Fluorescein Propiolate: a Propiolate- Decorated Fluorescent Probe With Remarkable Selectivity Towards Cysteine(Royal Society of Chemistry, 2019) Karakuş, Erman; Sayar, Melike; Kaya, Beraat Umur; Kaya, Beraat Umur; Emrullahoğlu, Mustafa; Dartar, Suay; Emrullahoğlu, Mustafa; 04.01. Department of Chemistry; 01. Izmir Institute of Technology; 04.04. Department of Photonics; 04. Faculty of ScienceA fluorescent probe decorated with an alkynyl ester unit (e.g. propiolate) displayed a selective turn-on type fluorescent response towards cysteine. Following a sequential addition-cyclisation pathway mediated by the addition of cysteine, the pre-fluorescent dye rapidly transformed into a new structure and induced a fluorescent response clearly observable with the naked eye.