Scopus İndeksli Yayınlar Koleksiyonu / Scopus Indexed Publications Collection
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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) Tarim, Burcu Sirma; Tamburaci, Sedef; Top, AybenHydrogel-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.Note Reply to the ‘Comment on “Shallow Shell SSTA63 Resin: A Rapid Approach To Remediation of Hazardous Nitrate”’ by K. H. Chu, Environ. Sci.: Water Res. Technol., 2026, 12, DOI: 10.1039/D4ew00976b(Royal Society of Chemistry, 2026) Çendik, E.; Saygı, M.; Recepoğlu, Y.K.; Arar, Ö.Corrections are provided for “Shallow Shell SSTA63 resin: a rapid approach to remediation of hazardous nitrate” (Çendik et al., Environ. Sci.: Water Res. Technol., 2024, 10, 2765–2775, https://doi.org/10.1039/D4EW00584H) in response to the comment by K. H. Chu (Environ. Sci.: Water Res. Technol., 2026, 12, https://doi.org/10.1039/D4EW00976B). This journal is © The Royal Society of Chemistry, 2026Article Citation - WoS: 3Citation - Scopus: 3Reusable polymer-based fluorescent sensor nanoprobe for selective detection of cd<sup>2+</sup> ions in real water sources(Royal Society of Chemistry, 2024) Karabıyık, Merve; Ebil, ÖzgençCadmium, which is classified as a highly toxic metal among all heavy metals, poses a threat to the environment and human health, even at trace levels. In this study, for the first time in the literature, a fluorescent sensor nanoprobe that can selectively detect Cd2+ ions in different real water sources has been developed by attaching a CdTe QD-4 amino TEMPO complex to an iCVD deposited cross-linked copolymer surface with high mechanical strength. Under the appropriate conditions such as pH, concentration, type of solvent and reaction time, the interaction between Cd2+ ions and the polymer-based QD-4AT nanoprobe was enhanced, and the detection of this target ion with high selectivity was made possible even in the environments with complex structures containing different heavy metal ions. The limit of detection (LOD) of Cd2+ ions with this proposed polymer sensor nanoprobe was found to be 0.195 mu M by using the linear detection region of 0.0784-2.5 mu M (R-2 > 0.997). In the literature, several sensor probes have been developed for the detection of Cd2+ ions and have only been investigated for single use in liquid media. The polymer sensor nanoprobe developed in this study has high sensitivity and selectivity in terms of detection limit compared to the previous ones, and the results obtained from the multiple use studies indicate that this nanoprobe can be used more than once for ion detection without loss of performance. This is a brand-new product for fluorescence sensing studies and will be a great source of inspiration for them.Article Citation - WoS: 3Citation - Scopus: 3Shallow Shell Ssta63 Resin: a Rapid Approach To Remediation of Hazardous Nitrate(Royal Society of Chemistry, 2024) Cendik, Elif; Saygi, Mugenur; Recepoğlu, Yaşar Kemal; Arar, OzgurThis study examines the potential of Purolite Shallow Shell (TM) SSTA63 anion exchange resin for mitigating nitrate ion (NO3-) contamination in aqueous environments. Through systematic experimentation, including dosage optimization, pH dependency, kinetic and desorption studies, we investigate the sorption behavior and practical applications of the resin. Results indicate that the resin effectively removes NO3- ions, with maximum efficiency achieved within 10 minutes. When 0.025 g of resin was used, 75% of NO3- was removed, whereas with 0.05 g, 89% was removed, and with 0.1 g of resin, 95% was removed. At pH 1, approximately 50% of NO3- ions were removed, with removal efficiency reaching 97% between pH 4 and 10. Sorption isotherms affirm the suitability of the Langmuir model for the current investigation. The monolayer maximum sorption capacity (qmax) value was found to be 53.65 mg g-1. The resin demonstrates robust desorption capabilities using 0.1 M hydrochloric acid (HCl), effectively desorbing NO3- above 99%, indicating easy NO3- desorption and resin regeneration. The presence of coexisting ions such as chloride (Cl-), sulfate (SO42-), and phosphate (PO43-) showed a minimal impact on NO3- removal in individual binary mixtures, with efficiencies exceeding 93%, suggesting a strong selectivity of the resin towards NO3-. Purolite SSTA63 anion exchange resin exhibited a high affinity for NO3- ions, even over other competing ions, despite the general trend of ion exchange resins to favor ions with a higher atomic number and valence. Overall, this resin presents a promising solution for NO3- removal, with implications for water treatment and environmental remediation. This study explores the potential of Purolite Shallow Shell (TM) SSTA63 anion exchange resin for mitigating nitrate ion (NO3-) contamination in aqueous environments.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.Herein 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: 14Citation - Scopus: 14Development of Tissue-Engineered Vascular Grafts From Decellularized Parsley Stems(Royal Society of Chemistry, 2023) Çevik, Merve; Dikici, SerkanCardiovascular diseases are mostly associated with narrowing or blockage of blood vessels, and it is the most common cause of death worldwide. The use of vascular grafts is a promising approach to bypass or replace the blocked vessels for long-term treatment. Although autologous arteries or veins are the most preferred tissue sources for vascular bypass, the limited presence and poor quality of autologous vessels necessitate seeking alternative biomaterials. Recently, synthetic grafts have gained attention as an alternative to autologous grafts. However, the high failure rate of synthetic grafts has been reported primarily due to thrombosis, atherosclerosis, intimal hyperplasia, or infection. Thrombosis, the main reason for failure upon implantation, is associated with damage or absence of endothelial cell lining in the vascular graft's luminal surface. To overcome this, tissue-engineered vascular grafts (TEVGs) have come into prominence. Alongside the well-established scaffold manufacturing techniques, decellularized plant-based constructs have recently gained significant importance and are an emerging field in tissue engineering and regenerative medicine. Accordingly, in this study, we demonstrated the fabrication of tubular scaffolds from decellularized parsley stems and recellularized them with human endothelial cells to be used as a potential TEVG. Our results suggested that the native plant DNA was successfully removed, and soft tubular biomaterials were successfully manufactured via the chemical decellularization of the parsley stems. The decellularized parsley stems showed suitable mechanical and biological properties to be used as a TEVG material, and they provided a suitable environment for the culture of human endothelial cells to attach and create a pseudo endothelium prior to implantation. This study is the first one to demonstrate the potential of the parsley stems to be used as a potential TEVG biomaterial. © 2024 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 EmreSpheroid 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.Review Citation - WoS: 14Citation - Scopus: 14Recent Advances in Lab-On Systems for Breast Cancer Metastasis Research(Royal Society of Chemistry, 2023) Fıratlıgil Yıldırır, Burcu; Yalçın Özuysal, Özden; NonappaBreast cancer is the leading cause of cancer-related deaths in women. Multiple molecular subtypes, heterogeneity, and their ability to metastasize from the primary site to distant organs make breast cancer challenging to diagnose, treat, and obtain the desired therapeutic outcome. As the clinical importance of metastasis is dramatically increasing, there is a need to develop sustainable in vitro preclinical platforms to investigate complex cellular processes. Traditional in vitro and in vivo models cannot mimic the highly complex and multistep process of metastasis. Rapid progress in micro- and nanofabrication has contributed to soft lithography or three-dimensional printing-based lab-on-a-chip (LOC) systems. LOC platforms, which mimic in vivo conditions, offer a more profound understanding of cellular events and allow novel preclinical models for personalized treatments. Their low cost, scalability, and efficiency have resulted in on-demand design platforms for cell, tissue, and organ-on-a-chip platforms. Such models can overcome the limitations of two- and three-dimensional cell culture models and the ethical challenges involved in animal models. This review provides an overview of breast cancer subtypes, various steps and factors involved in metastases, existing preclinical models, and representative examples of LOC systems used to study and understand breast cancer metastasis and diagnosis and as a platform to evaluate advanced nanomedicine for breast cancer metastasis.Article Citation - WoS: 1Citation - Scopus: 1A Multi-Layered Graphene Based Gas Sensor Platform for Discrimination of Volatile Organic Compounds Via Differential Intercalation(Royal Society of Chemistry, 2023) Özkendir İnanç, Dilce; Ng, Zhi Kai; Başkurt, Mehmet; Keleş, Berfin; Vardar, Gökay; Şahin, Hasan; Tsang, Siu Hon; Palaniappan, Alagappan; Yıldız, Ümit Hakan; Teo, EhtSelective and sensitive detection of volatile organic compounds (VOCs) is of critical importance for environmental monitoring, disease diagnosis and industrial applications. Among VOCs, assay development for primary alcohols has captured significant research attention since their toxicity causes adverse effects on gastrointestinal and central nerve systems, resulting in irreversible blindness, and coma, and can be even fatal at high exposure levels. However, selective detection of primary alcohols is extremely challenging owing to the similarity in their molecular structure and characteristic groups. Herein, we have attempted to investigate the differential methanol (MeOH)-ethanol (EtOH) discriminative properties of single-layer, bi-layer, and multi-layer graphene morphologies. Chemiresistors fabricated using the three morphologies of graphene illustrate discriminative MeOH-EtOH responses, which is attributed to the phenomenon of differential intercalation of MeOH within layered graphene morphologies as compared to that of EtOH. This hypothesis is verified by density functional theory calculations, which revealed that the adsorption of EtOH molecules on the graphene surface is more energetically favorable as compared to that of MeOH molecules, thereby inhibiting their intercalation within the layered graphene morphologies. It is further evaluated that the degree of MeOH intercalation increases with increasing layers of graphene for obtaining differential MeOH-EtOH responses. Experimental results suggest possibilities to develop selective and sensitive MeOH assays fabricated using various graphene morphologies in a combinatorial sensor array format.Article Citation - WoS: 6Citation - Scopus: 6Polar Solvent-Free Room Temperature Synthesis of Cspbx3 (x = Br, Cl) Perovskite Nanocubes(Royal Society of Chemistry, 2023) Güvenç, Çetin Meriç; Kocabaş, Aşkın; Balcı, SinanConventionally, colloidal lead halide perovskite nanocubes have been synthesized by the hot-injection or ligand-assisted reprecipitation (LARP) methods. We herein demonstrate a polar solvent-free room temperature method for the synthesis of CsPbX3 (X = Br, Cl) nanocubes. In addition to the commonly used ligand pair of oleylamine and oleic acid, guanidinium (GA) has been used to passivate the surface of the nanocrystals. Our study demonstrates that GA inhibits the formation of low dimensional structures such as nanowires and nanoplatelets and further supports the formation of perovskite nanocubes. In fact, GA diminishes the restricted monomer-addition effect of long-chain oleylammonium (OLAM) ions to the nanocrystal. We show that above a critical GA/OLAM molar ratio, the synthesis yields homogeneous CsPbX3 (X = Br, Cl) nanocubes. Importantly, we observe the nucleation and growth kinetics of the GA-assisted CsPbBr3 nanocube formation by using in situ absorption and photoluminescence (PL) measurements. Small nanocrystals with an excitonic absorption peak at around 435 nm and photoluminescence (PL) maxima at 447 nm were nucleated and continuously shifted to longer wavelengths during the growth period. Crucially, our method allows the synthesis of CsPbCl3 nanocubes at room temperature without using polar organic solvents. The synthesized CsPbBr3, CsPb(Cl0.5Br0.5)3, and CsPbCl3 nanocubes have PL peaks at 508 nm, 443 nm, and 405 nm, photoluminescence quantum yields (PLQY) of 85%, 58% and 5%, and lifetimes of 18.98 ns, 18.97 ns, and 14.74 ns, respectively.