WoS İndeksli Yayınlar Koleksiyonu / WoS Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/11147/7150
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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: 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 - 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.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: 9Citation - Scopus: 9Fabrication and Development of a Microfluidic Paper-Based Immunosorbent Assay Platform (μpisa) for Colorimetric Detection of Hepatitis C(Royal Society of Chemistry, 2023) Özefe, Fatih; Arslan Yıldız, AhuPaper-based microfluidics is an emerging analysis tool used in various applications, especially in point-of-care (PoC) diagnostic applications, due to its advantages over other types of microfluidic devices in terms of simplicity in both production and operation, cost-effectiveness, rapid response time, low sample consumption, biocompatibility, and ease of disposal. Recently, various techniques have been developed and utilized for the fabrication of paper-based microfluidics, such as photolithography, micro-embossing, wax and PDMS printing, etc. In this study, we offer a fabrication methodology for a microfluidic paper-based immunosorbent assay (μPISA) platform and the detection of Hepatitis C Virus (HCV) was carried out to validate this platform. A laser ablation technique was utilized to form hydrophobic barriers easily and rapidly, which was the major advantage of the developed fabrication methodology. The characterization of the μPISA platform was performed in terms of micro-channel properties using bright-field (BF) microscopy, and surface properties using scanning electron microscopy (SEM). At the same time, sample volume and liquid handling capacity were analyzed quantitatively. Ablation speed (S) and laser power (P) were optimized, and it was shown that one combination (10P60S) provided minimal deviation in micro-channel dimensions and prevented deterioration of hydrophobic barriers. Also, the minimum hydrophobic barrier width, which prevents cross-barrier bleeding, was determined to be 255.92 ± 10.01 μm. Furthermore, colorimetric HCV NS3 detection was implemented to optimize and validate the μPISA platform. Here, HCV NS3 in both PBS and human blood plasma was successfully detected by the naked eye at concentrations as low as 1 ng mL−1 and 10 ng mL−1, respectively. Moreover, the limit of detection (LoD) values for HCV NS3 were acquired as 0.796 ng mL−1 in PBS and 2.203 ng mL−1 in human blood plasma with a turnaround time of 90 min. In comparison with conventional ELISA, highly sensitive and rapid HCV NS3 detection was accomplished colorimetrically on the developed μPISA platform.Article Citation - WoS: 3Citation - Scopus: 3Continuous Production of Hyperbranched Polyhydrocarbons by Electrochemical Polymerization of Chlorinated Methanes(Royal Society of Chemistry, 2022) Seo, Jae Hong; Nam, Hyun Ju; Rajendiran, Rajmohan; Seong, Won Kyung; Jiang, Yi; Kim, Min Hyeok; Büyükçakır, OnurA continuous production of polyhydrocarbon (PHC) by electrochemical polymerization of chlorinated hydrocarbons is presented. Monomer loading and product transfer were controlled by changing flow direction in a home-built continuous flow system that facilitates preparation, work-up, and scale-up of electrochemical polymerization. The polymerization can be tuned by adjusting reaction time, cell configuration, molar ratio of input chemicals, and the solvent type. CH2Cl2, CHCl3, and CCl4 were used to synthesize PHC. The reduction of the monomers at the cathode was studied by cyclic voltammetry and chronoamperometry. We investigated the structure and composition of PHCs from FT-IR and NMR spectra along with elemental analysis. Sufficient amounts of product are generated by continuous production and characterization of the product PHCs by a wide variety of methods is possible. Particularly, structural analysis by various C-13 NMR techniques suggests a new pathway for the synthesis of hyperbranched PHCs by electrochemical polymerization.Article Citation - WoS: 1Citation - Scopus: 1Inhibition of Caco3 Growth and Synthesis of Submicron Particles by Preferential Adsorption of Additive Ca2+ Ions on Fresh Precipitates(Royal Society of Chemistry, 2022) Majekodunmi, Olukayode T.; Kılıç Özdemir, Sevgi; Özdemir, EkremThis study demonstrates a method to inhibit the growth of CaCO3 and synthesize submicron particles in a chemical precipitation process under ambient and high supersaturation conditions. Equimolar CaCl2 and Na2CO3 solutions were mixed in a model tubular reactor at a constant flow rate, and the precipitates were continuously dispersed in stirred 250 mL of 10 mM Ca(OH)2 solution. This approach resulted in the synthesis of colloidally stable submicron CaCO3 particles for a precipitant concentration ≤75 mM. Varying the precipitates’ retention time in the tubular reactor had no significant effects on the particle size and colloidal stability. Time-dependent changes in the mean size, crystal form, morphology and specific surface area of the synthesized particles were also studied. For a precipitant concentration of 75 mM, the particles were monodispersed and porous spindle-like scalenohedral crystals which gradually grew in all faces as more precipitates were fed into the Ca(OH)2 solution. The mean hydrodynamic size of the particles was ∼850 nm at the 8th minute. However, in the absence of additive Ca2+ ions, the particles obtained at the 8th minute were polydisperse mixtures of vaterite and rhombohedral calcite particles greater than 4 μm in size. The results show that free additive Ca2+ ions are irreversibly adsorbed onto the particles as the precipitates dissolve and recrystallize into smaller crystals upon reaching the Ca(OH)2 solution.Article Citation - WoS: 2Citation - Scopus: 2High-Throughput Analysis of Tetragonal Transition Metal Xenes(Royal Society of Chemistry, 2022) Šabani, Denis; Milošević, Milorad V.; Yorulmaz, Uğur; Yağmurcukardeş, Mehmet; Sevik, CemWe report a high-throughput first-principles characterization of the structural, mechanical, electronic, and vibrational properties of tetragonal single-layer transition metal Xenes (t-TMXs). Our calculations revealed 22 dynamically, mechanically and chemically stable structures among the 96 possible free-standing layers present in the t-TMX family. As a fingerprint for their structural identification, we identified four characteristic Raman active phonon modes, namely three in-plane and one out-of-plane optical branches, with various intensities and frequencies depending on the material in question. Spin-polarized electronic calculations demonstrated that anti-ferromagnetic (AFM) metals, ferromagnetic (FM) metals, AFM semiconductors, and non-magnetic semiconductor materials exist within this family, evidencing the potential of t-TMXs for further use in multifunctional heterostructures.Article Citation - WoS: 5Citation - Scopus: 5Structural Analysis of Hyperbranched Polyhydrocarbon Synthesized by Electrochemical Polymerization(Royal Society of Chemistry, 2022) Jiang, Yi; Kim, Minhyeok; Nam, Hyunju; Kwak, Sang Kyu; Ruoff, Rodney S.; Lee, Sun Hwa; Seo, Jae Hong; Shin, Eunhye; Joo, Se Hun; Büyükçakır, OnurWe describe a structural analysis method for a hyperbranched polyhydrocarbon (PHC) produced by electrochemical polymerization. Nuclear magnetic resonance (NMR) techniques including 1H-NMR, quantitative 13C-NMR, DEPT 13C-NMR, and 1H-13C HSQC 2D NMR along with elemental analysis and FTIR were used to experimentally assess the likely structure of this complex polymer with random branching. The polymer structure was modeled based on the NMR results. Room temperature density, refractive index, melting temperature, and IR spectrum were good matches to the values, and spectrum, calculated using the simulated structure. Calculated Hildebrand solubility parameters for the simulated structure rationalize the room temperature solubility measured in a range of solvents. The experimental and modeling methods are likely to be applicable to any type of highly branched random branching polymer. To the best of our knowledge, this is the first comprehensive elucidation of the structure of an unknown and randomly hyperbranched polymer by combining experimental results and theoretical simulation, and the methods described should find broad use in the future.