Scopus İndeksli Yayınlar Koleksiyonu / Scopus Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/11147/7148
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Article Self-Assembled Peptide Hydrogels with Cell Attachment Motifs for 3D Lung Cancer Model: Evaluation of Cell-Matrix Interactions and Drug Response(John Wiley and Sons Inc, 2026) Sırma Tarım, B.; Tamburaci, S.; Top, A.3D cancer models can mimic the tumor microenvironment, serving as a physiologically relevant platform to investigate the behavior of tumors and test anticancer therapeutics. Although bioactive peptide hydrogels have been widely evaluated for tissue engineering applications, their potential in 3D cancer models has been confirmed in only a few studies. In this study, self-assembling peptide hydrogels containing LDV (IBP1) and LDV and IKVAV cell attachment motifs (IBP2), and the control hydrogel without adhesion units (KLEI) were used for lung cancer modeling. The peptides self-assembled into hydrogels in a cell culture medium with storage moduli of ∼700–1500 Pa. The IBP1 and IBP2 hydrogels enhanced A549 cell proliferation and induced the formation of spheroids with average diameters between ∼70 and ∼150 µm. The cells in KLEI hydrogel with the highest stiffness exhibited mesenchymal-type migration, independent of the cell population, whereas transformation to mesenchymal migration necessitated a specific cell population in the IBP2 hydrogel. The cells in the IBP1 and IBP2 hydrogels with enhanced cell-cell interactions demonstrated higher resistance to docetaxel (DTX). Thus, our results indicate that these bioactive hydrogels can serve as a promising platform for in vitro assessment of cancer mechanisms and drug screening. © 2026 Wiley-VCH GmbH.Article Epigallocatechin Gallate and Punicalagin Combination Reduces Aβ Aggregation and Promotes Neurogenesis in Adult Zebrafish Brain(John Wiley and Sons Inc, 2026) Nazli, D.; Ipekgil, D.; Poyraz, Y.K.; Can, K.; Okmen, I.; Turhanlar-Sahin, E.; Ozhan, G.Alzheimer's disease (AD) is a progressive neurodegenerative disorder characterized by cognitive decline, memory impairment, and behavioral alterations. The pathogenesis of AD involves the accumulation of amyloid-beta (Aβ) plaques and the hyperphosphorylated tau proteins, which disrupt neuronal function and trigger neuroinflammation. This study explores the therapeutic potential of epigallocatechin gallate (EGCG) and punicalagin (PU) in mitigating Aβ-induced toxicity using an adult zebrafish model of AD. Our results demonstrate that the EGCG + PU combination significantly reduces Aβ accumulation, protects against cellular damage, suppresses acetylcholinesterase (AChE) activity, and normalizes the expression of amyloidogenic and AD-related genes. Additionally, EGCG + PU treatment alleviates neuroinflammation by suppressing glial activation, including reductions in L-plastin and proinflammatory cytokine expression, while promoting neuronal recovery through mechanisms of neurogenesis and neuroprotection. Notably, the combination treatment restored neuronal density and improved behavioral outcomes by alleviating anxiety- and aggression-like behaviors associated with Aβ toxicity. These results underscore the synergistic neuroprotective effects of EGCG + PU, highlighting their potential as a novel therapeutic approach for mitigating the pathological, behavioral, and inflammatory aspects of AD. © 2026 Wiley Periodicals LLC.Article Tuning Pore Chemistry in Dioxin-Linked Porous Organic Polymers for Enhanced High-Pressure CO2 Uptake(John Wiley and Sons Inc, 2025) Ashirov, T.; Piech, K.; Büyükcakir, O.; Yildirim, T.; Coskun, A.Precise tuning of pore chemistry in three-dimensional porous organic polymers (3D-POPs) is critical for high-performance gas (CO<inf>2</inf>)-separation. Here, we demonstrate the impact of functional groups on the dioxin-linked 3D-tPOPs bearing a tetraphenylene core, synthesized under solvothermal conditions using NaCl as a template, on the low- and high-pressure CO<inf>2</inf> uptake. The post-synthetic amidoxime functionalization of 3D-tPOPs, involving the reaction of pendant nitrile moieties with hydroxylamine hydrochloride, has been shown to precisely tailor pore chemistry without altering the network structure. Whereas the incorporation of the amidoxime moieties, 3D-tPOP-AO, enables higher heteroatom content, a critical factor to enhance CO<inf>2</inf> affinity at low pressures, strong hydrogen bonding interactions between amidoxime units limit framework flexibility, thus leading to a significant decrease in the high-pressure gas uptake. 3D-tPOPs on the other hand showed a high CO<inf>2</inf> uptake capacity of 57.4 wt% at 33 bar and 270 K; after modification, CO<inf>2</inf> uptake capacity decreased to 19.4 wt% at 273 K and 34 bar. Similarly, CH<inf>4</inf> uptake capacity also decreased from 14.0 wt% at 116 bar and 270 K to 3.8 wt% at 75 bar and 273 K. These findings highlight the critical role of the interactions between functional groups and pore chemistry to form robust adsorbents with high CO<inf>2</inf> uptake performance at high pressures. © 2025 The Author(s). Helvetica Chimica Acta published by Wiley-VHCA AG.Article Citation - WoS: 3Citation - Scopus: 4Evaluation of in Vivo and in Vitro Toxicity of Chestnut (Castanea Mollissima Blume) Plant: Developmental Toxicity in Zebrafish Embryos Cytotoxicity, Antioxidant Activity, and Phytochemical Composition by LC-ESI-MS/MS(John Wiley and Sons Inc, 2025) Demirtas, Ibrahim; Atalar, Mehmet Nuri; Bingol, Zeynebe; Kokturk, Mine; Ozhan, Gunes; Abdelsalam, Amine Hafis; Gulcin, IlhamiThe search for novel therapeutic agents has led to increasing interest in natural products, driven by the recognition that they may offer safer and more sustainable alternatives to synthetic drugs. This study aims to fill the gap in knowledge regarding the biological activity and safety of the water extract of chestnut (Castanea mollissima) (chestnut), a plant species with a long history of use in traditional medicine, by conducting a comprehensive evaluation of its antioxidant, antidiabetic, and neuroprotective properties. This study presents a comprehensive analysis of the water extract of chestnut for the first time using various bioanalytical antioxidant methods. The extract's inhibitory effects on key enzymes like acetylcholinesterase (AChE), butyrylcholinesterase (BChE), and alpha-glycosidase were evaluated due to their relevance in metabolic and neurodegenerative disorders such as diabetes and Alzheimer's disease. Developmental toxicity and cytotoxicity were assessed using zebrafish (Danio rerio) embryos to evaluate the extract's biological safety. The major phenolic compounds present in the extract were identified by liquid chromatography-electrospray ionization tandem mass spectrometry (LC-ESI-MS/MS), revealing catechin, gallic acid, taxifolin, and epicatechin as the predominant constituents. Antioxidant capacity was determined through radical scavenging assays using 2,2-diphenyl-1-picrylhydrazyl (DPPH center dot) and 2,2 '-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS center dot+), alongside ferric (Fe3+), cupric (Cu2+), and Fe3+-TPTZ (ferric-tripyridyltriazine) reducing power assays. The findings highlight the significant antioxidant, antidiabetic, and neuroprotective potential of the chestnut water extract, supporting its prospective use in pharmaceutical and nutraceutical applications.Article Citation - WoS: 1Citation - Scopus: 1Gate-Controlled Photoresponse in an Individual Single-Walled Carbon Nanotube Modified With a Fluorescent Protein(John Wiley and Sons Inc, 2025) Kudriavtseva, A.S.; Nekrasov, N.P.; Krasnikov, D.V.; Nasibulin, A.G.; Bogdanov, A.M.; Bobrinetskiy, I.Bionanohybrids of carbon nanotubes and fluorescent proteins (FPs) are a promising class of materials for optoelectronic applications. Understanding and controlling the charge transport mechanism between FPs and carbon nanotubes are critical to achieving functional reproducibility and exploring novel synergetic effects. This work demonstrates a novel phenomenon of photocurrent generation in field-effect transistors based on the conjugation of an individual single-walled carbon nanotube (SWCNT) and FPs. When studying the effect of gate voltage on the photoresponse, reversible switching from fast positive to a slow negative photoresponse in bionanohybrids associated with depletion and accumulation modes, respectively is observed. The latter demonstrates a stable memory effect after the light is turned off. It is revealed that in depletion mode, the charge carriers from the protein are not trapped at the interface due to effective screening by the gate potential. It is suggested that the main mechanism in photoresponse switching is a competitive effect between photogating and effective photodoping of the SWCNT by charges trapped at the nanotube interface. The noticeable effect of water molecules can support proton transfer as the main mechanism of charge transfer. This result illustrates that SWCNT/FP bionanohybrids bear great potential for the realization of novel optoelectronic devices. © 2024 The Author(s). Advanced Electronic Materials published by Wiley-VCH GmbH.Article Citation - WoS: 5Citation - Scopus: 8Textural, Rheological, Melting Properties, Particle Size Distribution, and Nmr Relaxometry of Cocoa Hazelnut Spread With Inulin-Stevia Addition as Sugar Replacer(John Wiley and Sons Inc, 2024) Berk,B.; Cosar,S.; Mazı,B.G.; Oztop,M.H.This study investigated the influence of substituting 60, 80, and 100% of the sugar in traditional cocoa hazelnut paste (control) formulation with inulin-stevia (90:10, w/w) mixture on textural and rheological characteristics, melting behavior, water activity (aw), particle size distribution (PSD), and color. Textural, rheological, melting properties, and color of samples were analyzed after 1, 2, and 3 months of storage at 11°C. Nuclear magnetic resonance (NMR) relaxometry experiments were also performed to understand the interaction of new ingredients with oil. Replacement of sugar with inulin-stevia gave darker color, reduced Casson yield stress, and changed the textural parameters and melting profile of the samples depending on the level but did not create a remarkable effect on PSD and Casson plastic viscosity. Increasing inulin-stevia content yielded lower aw and higher T2a values indicating decreased mobility of water. Complete removal of sugar caused low spreadability. The results showed that an 80% replacement level yielded a product with similar textural parameters and fat-melting mouth feeling compared to control sample. Cocoa hazelnut spreads prepared with inulin and stevia showed good textural stability during storage. © 2024 The Authors. Journal of Texture Studies published by Wiley Periodicals LLC.Article Effect of Irradiation on Total Biophenol and Antioxidant Activity During Storage of Natural Black Table Olives Obtained Using Starter Culture(John Wiley and Sons Inc, 2024) Irmak,Ş.; Öztürk Güngör,F.; Susamci,E.; Sevim,D.; Köseoğlu,O.In this study, it was aimed to determine the effects of different production and preservation methods on the shelf life and quality of the Gemlik variety of natural black table olives produced with low salt (2%). For this purpose, olives were processed by the traditional Turkish style dry salted black olive by using a starter culture. The MAP (Modified atmosphere packaging, 60% N2 and 40% CO2), vacuum and for the first time gamma irradiation methods (1, 3 and 5 kGy) were applied in the preservation of table olives. The 5 kGy irradiation treatment reduced the total phenolic amount and DPPH antioxidant activity of olives more than other irradiation doses. The pH (4.3–4.83) and titratable acidity (0.68–1.02%) of the samples changed in accordance with the legal regulations during the storage period (pH max. 5 and acidity min 0.3%). At the end of the fermentation and storage, total phenolic content and antioxidant activity decreased significantly (p-value <0.05). During the storage period, the total phenolic content in natural fermented olives (without starter culture) decreased from 232 to 144 mgCAE/100 g and in starter culture added table olives from 200 to 138 mgCAE/100 g. In addition, the antioxidant activity was changed between 60.94 and 47.14 μmolTE/100 g oil. As a result of the study, it was ensured that black table olives produced with less salt (2%) could be stored on the shelves for 6 months without using any preservatives. In addition, radiation effect on quality was relatively similar to other treatments (vacuum and MAP). © 2024 AOCS.Article Citation - Scopus: 6Sequence Identification and in Silico Characterization of Novel Thermophilic Lipases From Geobacillus Species(John Wiley and Sons Inc, 2024) Sürmeli,Y.; Tekedar,H.C.; Şanlı-Mohamed,G.Microbial lipases are utilized in various biotechnological areas, including pharmaceuticals, food, biodiesel, and detergents. In this study, we cloned and sequenced Lip21 and Lip33 genes from Geobacillus sp. GS21 and Geobacillus sp. GS33, then we in silico and experimentally analyzed the encoded lipases. For this purpose, Lip21 and Lip33 were cloned, sequenced, and their amino acid sequences were investigated for determination of biophysicochemical characteristics, evolutionary relationships, and sequence similarities. 3D models were built and computationally affirmed by various bioinformatics tools, and enzyme-ligand interactions were investigated by docking analysis using six ligands. Biophysicochemical property of Lip21 and Lip33 was also determined experimentally and the results demonstrated that they had similar isoelectric point (pI) (6.21) and Tm (75.5°C) values as Tm was revealed by denatured protein analysis of the circular dichroism spectrum and pI was obtained by isoelectric focusing. Phylogeny analysis indicated that Lip21 and Lip33 were the closest to lipases from Geobacillus sp. SBS-4S and Geobacillus thermoleovorans, respectively. Alignment analysis demonstrated that S144–D348–H389 was catalytic triad residues in Lip21 and Lip33, and enzymes possessed a conserved Gly-X-Ser-X-Gly motif containing catalytic serine. 3D structure analysis indicated that Lip21 and Lip33 highly resembled each other and they were α/β hydrolase-fold enzymes with large lid domains. BANΔIT analysis results showed that Lip21 and Lip33 had higher thermal stability, compared to other thermostable Geobacillus lipases. Docking results revealed that Lip21- and Lip33-docked complexes possessed common residues (H112, K115, Q162, E163, and S141) that interacted with the substrates, except paranitrophenyl (pNP)-C10 and pNP-C12, indicating that these residues might have a significant action on medium and short-chain fatty acid esters. Thus, Lip21 and Lip33 can be potential candidates for different industrial applications. © 2023 International Union of Biochemistry and Molecular Biology, Inc.Review Citation - Scopus: 33Molecular Separation by Using Active and Passive Microfluidic Chip Designs: a Comprehensive Review(John Wiley and Sons Inc, 2024) Ebrahimi,A.; Icoz,K.; Didarian,R.; Shih,C.-H.; Tarim,E.A.; Nasseri,B.; Avci,H.Separation and identification of molecules and biomolecules such as nucleic acids, proteins, and polysaccharides from complex fluids are known to be important due to unmet needs in various applications. Generally, many different separation techniques, including chromatography, electrophoresis, and magnetophoresis, have been developed to identify the target molecules precisely. However, these techniques are expensive and time consuming. “Lab-on-a-chip” systems with low cost per device, quick analysis capabilities, and minimal sample consumption seem to be ideal candidates for separating particles, cells, blood samples, and molecules. From this perspective, different microfluidic-based techniques have been extensively developed in the past two decades to separate samples with different origins. In this review, “lab-on-a-chip” methods by passive, active, and hybrid approaches for the separation of biomolecules developed in the past decade are comprehensively discussed. Due to the wide variety in the field, it will be impossible to cover every facet of the subject. Therefore, this review paper covers passive and active methods generally used for biomolecule separation. Then, an investigation of the combined sophisticated methods is highlighted. The spotlight also will be shined on the elegance of separation successes in recent years, and the remainder of the article explores how these permit the development of novel techniques. © 2023 The Authors. Advanced Materials Interfaces published by Wiley-VCH GmbH.Article Citation - Scopus: 6Functional Characterization of a Novel Cyp119 Variant To Explore Its Biocatalytic Potential(John Wiley and Sons Inc, 2022) Sakalli, T.; Surmeli, N.B.Biocatalysts are increasingly applied in the pharmaceutical and chemical industry. Cytochrome P450 enzymes (P450s) are valuable biocatalysts due to their ability to hydroxylate unactivated carbon atoms using molecular oxygen. P450s catalyze reactions using nicotinamide adenine dinucleotide phosphate (NAD(P)H) cofactor and electron transfer proteins. Alternatively, P450s can utilize hydrogen peroxide (H2O2) as an oxidant, but this pathway is inefficient. P450s that show higher efficiency with peroxides are sought after in industrial applications. P450s from thermophilic organisms have more potential applications as they are stable toward high temperature, high and low pH, and organic solvents. CYP119 is an acidothermophilic P450 from Sulfolobus acidocaldarius. In our previous study, a novel T213R/T214I (double mutant [DM]) variant of CYP119 was obtained by screening a mutant library for higher peroxidation activity utilizing H2O2. Here, we characterized the substrate scope; stability toward peroxides; and temperature and organic solvent tolerance of DM CYP119 to identify its potential as an industrial biocatalyst. DM CYP119 displayed higher stability than wild-type (WT) CYP119 toward organic peroxides. It shows higher peroxidation activity for non-natural substrates and higher affinity for progesterone and other bioactive potential substrates compared to WT CYP119. DM CYP119 emerges as a new biocatalyst with a wide range of potential applications in the pharmaceutical and chemical industry. © 2021 International Union of Biochemistry and Molecular Biology, Inc.