Scopus İndeksli Yayınlar Koleksiyonu / Scopus Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/11147/7148
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Article Citation - WoS: 1Citation - Scopus: 1Biophysical Assessment of Protein Stability in Ethanol-Stressed Environments via UV Absorption and Fluorescence Spectroscopies(Elsevier, 2026) Akyuz, Ersed; Vorob'ev, Mikhail M.; Guler, GunnurMaintaining the structure and functionality of proteins is crucial in applications ranging from food preservation to pharmaceutical formulation. Ethanol, while commonly used as a solvent and preservative, can induce structural changes in proteins depending on its concentration and the specific structure of the protein itself. This study investigates the structural effects of ethanol on three types of model proteins, namely bovine serum albumin (BSA), beta-Lactoglobulin (beta-Lg), and beta-Casein (beta-Cn), by using UV-Vis spectroscopy and fluorescence spectroscopy. The conformational responses of proteins in water-EtOH solutions of various ethanol concentrations (0-10 %, v/v) were analyzed through absorbance and emission spectral changes. At increasing ethanol concentration, UV absorption data showed distinct protein-dependent spectral changes. beta-Lg and beta-Cn exhibited strong hypochromism (an absorbance decrease of similar to 25 %) and red-shifting at 222 nm and 220 nm, respectively, indicating partial unfolding and solvent exposure of aromatic residues. BSA demonstrated subtle changes, and consistent quenching in fluorescence with a continuous blue-shifting to 330 nm, suggesting a moderate overall stability and local rearrangements in its structure. beta-Cn exhibited red-shifted fluorescence and quenching, reflecting its flexible, disordered structure and heterogeneous response to solvent conditions. Statistical analysis revealed that while fluorescence spectroscopy was highly sensitive to the intrinsic differences between proteins (p < 0.001), the ethanol-induced conformational changes were too subtle to be detected as a statistically significant treatment effect. The consistency of these trends indicates a rational underlying mechanism of interaction. This reflects the subtle nature of the effect at the tested concentrations rather than the absence of an effect. Moreover, these results unveil the protein-specific effects of ethanol and strongly emphasize the importance of solvent composition in maintaining protein integrity. Ethanol concentrations up to 5 % may offer protein stability whereas high ethanol levels (>= 5-10 %) promote structural perturbations. These results will be useful for both basic scientific research, such as biophysical studies and the advancement of optical techniques, and various industrial uses.Article Residue-Specific Pathways in Peptide Fragmentation: the Role of Aromatic Side Chain in A3 Ion Formation From B3 Ion(Elsevier, 2025) Atik, A. Emin; Yalçın, Talat; Karaca, Sila; Yalcin, TalatPeptide fragmentation chemistry is essential for the sequence elucidation of proteins through tandem mass spectrometry (MS/MS). In this study, we examine the gas-phase fragmentation of b3 ions from model tripeptides under low-energy CID conditions, focusing on the pathway leading to the stable formation of a3 ions from b3 ions. The study utilized C-terminal amidated model tripeptides, including YGG-NH2, GYG-NH2, and GGX-NH2, where X represents D, E, H, Q, C, S, F, and Y. Our results reveal that only tripeptides with phenylalanine (F) and tyrosine (Y) as the third residue yield a3 ions upon b3 ion fragmentation under the applied experimental conditions, suggesting a unique stabilizing role of aromatic side chains in facilitating this pathway. Our theoretical studies indicate that the a3 ions from GGF-NH2 and GGY-NH2 preferentially adopt an energetically favored linear imineprotonated isomer, which is lower in energy by 3.29 kcal/mol and 4.17 kcal/mol, respectively, compared to their 7-membered ring isomers protonated at the ring imine. The latter structure has been previously assigned for the GGG sequence as a predominant structure, supported by IR spectroscopy and DFT calculations (JACS, 2010, 132, 14,766-14779). We proposed a plausible fragmentation mechanism for the a3 ions based on the linear imineprotonated structure. These findings provide insights into residue-specific fragmentation mechanisms and enhance our understanding of peptide ion dissociation, particularly in small peptides.Article Citation - WoS: 2Citation - Scopus: 2The Compaction Behavior of Magnesium-Expanded Natural Graphite Powder Mixtures: Tensile Strengths of Compacted Pellets(Elsevier, 2024) Guden, Mustafa; Betin, Bahattin Berkan; Heptepe, Cafer Can; Gulec, Efe Bati; Yagci, Yavuz Emre; Figen, Aysel Kanturk; Filiz, Bilge CoskunerThe effects of Expanded Natural Graphite (ENG) content, powder mixing method and compaction pressure on the tensile strengths of Magnesium AZ91 (9 wt% Al, 1 wt% Zn and 0.2 wt% Mn) + ENG powder mixture pellets were investigated. The tensile strengths of the pellets increased with an increase in the ENG content and compaction pressure and also with the applied powder ball milling. However, the compaction pressures above 500 MPa resulted in shear banding.Article Citation - WoS: 1Citation - Scopus: 1Canine Oocyte Nuclear Maturation With Nano-Ozone (nzs) Supplementation: the Alterations of Antioxidant, and Oxidant Status and Cdk1, Cyclin B1 Expressions(Elsevier, 2024) Bari, O.; Sabanci, A. U.; Avci, G.; Bozkurt, B.; Ustuner, B.; Denk, B.; Ozalp, G. R.This study aims to evaluate the effects of nano-ozone solution (NZS) on canine oocyte nuclear maturation, associated with the alterations of antioxidant and oxidant status and cyclin-dependent kinase 1 (CDK1), cyclin B1 gene expressions. Oocytes were cultured in four distinct concentrations of NZS (0.5, 1, 2, and 5 mu g/mL) and parthenogenetically activated. The rates of oocytes arrested at the Germinal Vesicle (GV), Germinal Vesicle Breakdown (GVBD), Metaphase I (MI), and Metaphase II (MII) stages were statistically different among groups (P < 0.05). The oocytes cultured in 1 <mu>g/mL NZS yielded the best oocyte maturation rate at the MI and MII stages; however, the lowest maturation and high degeneration rates were observed in Group E. The measurements of Malondialdehyde (MDA), reduced Glutathione (GSH), Superoxide Dismutase (SOD), and Ferric Reducing/Antioxidant Power assay (FRAP) were performed from IVM culture media. No statistical difference was observed in SOD and MDA results (P > 0.05). GSH levels were statistically significant between Group AGroup E (p = 0.003), Group B-Group E (p = 0.045), and Group E-Group D (p = 0.021). The culture media in Group D and Group E had high FRAP concentrations and significantly differed between groups (P < 0.05). CDK1, and cyclin B1 genes, which are subunits of maturation-promoting factor (MPF), are upregulated in Group B and Group C, while are downregulated in oocytes of Group E. This study showed that low, controlled doses of NZS (1 <mu>g/mL) supplementation could improve the meiotic competence of canine oocytes and lead to positive response in expressions of CDK1 and cyclin B1 on the gene level.Article Citation - WoS: 1Citation - Scopus: 1Protein Quantification Via Lspr-Based Biosensor Platform Utilizing Chrono-Growth for Enhanced Sensitivity(Elsevier, 2024) Sozmen, A. B.; Arslan-Yildiz, A.In this study an enhancement methodology, which utilizes time dependent growth of immobilized gold nanoparticles (GNPs) for LSPR-based biosensor platform was developed. The chrono-growth methodology was used for protein analysis and quantification. The method consisted GNP immobilization onto well-plates, GNP chronogrowth, and antibody functionalization. Success of each step was verified by UV-Vis spectrum measurement. Afterwards, the biosensor platform was tested to determine its characteristics. Bovine Serum Albumin (BSA) was chosen to be used as a model protein and an LoD value of 0.344 mu M and a dynamic detection range of 1 to 1000 mu M was calculated. The results were acquired within 30 min. Developed platform provides simple and rapid detection of the protein.Letter Citation - WoS: 1Citation - Scopus: 1Evaluating Ethanol Concentrations Against Staphylococcus Spp: a Proposal for Improving Nosocomial Bacteria Control(Elsevier, 2024) Soyer, Ferda; Özdemir, Özgün Öykü; Polat, Bengi; Ekenel, Nil HazalDear Editor, Nosocomial infections originating from commonly encountered pathogenic bacteria, notably Staphylococcus species, persist as a prominent global public health issue. This phenomenon exerts consequential impacts on both the well-being of patients and the healthcare personnel within hospital environments. Hospital-acquired infections from common bacteria like Staphylococcus remain a global public health concern. The European Centre for Disease Prevention and Control reports prevalence rates of 4.5% in the USA and 7.1% in Europe [1]. An estimated 8.9 million healthcare-associated infections occur annually in European hospitals and long-term care facilities [1]. According to the World Health Organization, although 10% of patients get healthcare-associated infections, at least a 30% reduction can be achieved through adequate infection prevention and control [2]. The efficacy of disinfection methodologies employed in healthcare institutions assumes critical significance in mitigating this threat.Article Mitotyping of Random Bred Cats and Pure Breed Cats (turkish Angora and Turkish Van) Using Non-Repetitive Mitochondrial Dna Control Region(Elsevier, 2024) Bilgen, Nuket; Guvendi, Mervenur; Sezgin, Efe; Can, Huseyin; Koseoglu, Ahmet Efe; Alak, Sedef Erkunt; Un, CemalThe Fertile Crescent appears to be the most plausible region where the domestication of cats commenced through a mutually beneficial relationship between wild cats and early agrarian societies. These domesticated cats then journeyed across the globe mirroring the paths of human migration. An examination of mitochondrial DNA (mtDNA) control region-based mitotyping suggested that a significant majority, exceeding 80%, of globally sampled random-bred and pure-bred cats could be categorized into 12 predominant mitotypes. However, the extent of mitotype diversity within random-bred cats from regions proximate to the Fertile Crescent remains inadequately explored. In light of this we aimed to investigate the mitotype diversity in random bred cats sampled from various regions across Turkey. Additionally, we sought to establish a comparison with the mito-type profiles of locally recognized pure breeds, namely the Turkish Angora and Turkish Van. To unravel their evolutionary narratives, we engaged in comprehensive population genetics analyses at both the individual and mitotype-based levels. Our study encompassed a sample size of 240 specimens, forming the basis for both mitotyping and population genetics scrutiny. Our analysis yielded the identification of nine 'universal' mitotypes (A-J), alongside an 'outlier' mitotype group I. Notably mitotypes A and D emerged as particularly prevalent in contrast to the lesser occurrence mitotypes C, G, and H. With the realm of random bred cats the structure of haplotypes exhibited remarkable diversity presenting distinctions from Turkish Angora and Van breeds. Nucleotide diversity was higher compared to previous reports from Turkey and was one of the highest among reported world cat population estimates. Intriguingly, our investigations did not unveil any pronounced instances of strong selection, population expansions or contractions within any specific population or mitotype. To conclude, our study represents a pioneering effort in uncovering the mitotype profiles and haplotype structures inherent to both random-bred and pure breed cats in Turkey. This endeavor not only broadens our understanding of the feline genetic landscape within the region but also lays the foundation for future inquiries into the evolutionary trajectories and genetic legacies of these feline populations.Article Citation - WoS: 1Citation - Scopus: 1Epoxy Matrix Nano Composites: Modulus, Strength and Ductility Enhancement Through Auxeticity of Α-Cristobalite Filler(Elsevier, 2023) Güden, Mustafa; Ülker, Sevkan; Movahedi, NimaThe negative Poisson's ratio (NPR) nano-size ?-Cristobalite particle/epoxy composites were prepared and tensile tested. The elastic modulus and strength of the composites were improved as the particle volume fraction increased from 0 to 0.02. Unlike the conventional particle reinforced composites, the fracture strain increased with the nano ?-Cristobalite addition, an effect which was ascribed to the intrinsic NPR behavior of the filler. © 2023 Elsevier B.V.Article Citation - WoS: 8Citation - Scopus: 9Dynamic Computational Wear Model of Peek-On Bearing Couple in Total Hip Replacements(Elsevier, 2023) Alpkaya, Alican Tuncay; Mihçin, ŞenayUnderstanding wear mechanisms is a key factor to prevent primary failures causing revision surgery in total hip replacement (THR) applications. This study introduces a wear prediction model of (Polyetheretherketone) PEEK-on-XLPE (cross-linked polyethylene) bearing couple utilized to investigate the wear mechanism under 3D-gait cycle loading over 5 million cycles (Mc). A 32-mm PEEK femoral head and 4-mm thick XLPE bearing liner with a 3-mm PEEK shell are modeled in a 3D explicit finite element modeling (FEM) program. The volumetric and linear wear rates of XLPE liner per every million cycles were predicted as 1.965 mm3/Mc, and 0.0032 mm/Mc respectively. These results are consistent with the literature. PEEK-on-XLPE bearing couple exhibits a promising wear performance used in THR application. The wear pattern evolution of the model is similar to that of conventional polyethylene liners. Therefore, PEEK could be proposed as an alternative material to the CoCr head, especially used in XLPE-bearing couples. The wear prediction model could be utilized to improve the design parameters with the aim of prolonging the life span of hip implants. © 2023Article Citation - WoS: 5Citation - Scopus: 5Thickness-Dependent Piezoelecticity of Black Arsenic From Few-Layer To Monolayer(Elsevier, 2023) Akgenç Hanedar, Berna; Ersan, Fatih; Altalhi, Tariq; Yağmurcukardeş, Mehmet; Yakobson, BorisUltra-thin forms of black phosphorus (b-P) have been widely investigated due to its unique properties arising from the in-plane anisotropy in its crystal structure. Recently, two-dimensional (2D) forms of black arsenic (b-As) have also been added to the 2D family. In this study, the thickness-dependent structural, electronic, and piezoelectric properties of layered b-As are investigated by means of ab-initio calculations. The structural optimizations confirm the van der Waals type layered structure for both these structures. In addition, increasing the thickness is shown to result in the decreasing of the band gap arising from the confinement of electrons in the layers. In contrast to the case of b-P, it is revealed that a transition from indirect-to-direct band gap behavior can be found in b-As which can be important for optically identifying the single-layer structure. Moreover, the piezoelectric properties are investigated as a function of the number of layers. It is shown that while a single-layer of b-As does not exhibit piezoelectric features, even in the case of bilayer structures the piezoelectricity is created. Our results revealed the strong in-plane anisotropy in piezoelectric coefficients for the three-layer and thicker structures. We have shown that the out-of-plane piezoelectric properties can be achieved by non-centrosymmetric features in the out-of-plane direction in thicker structures of b-As.
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