Scopus İndeksli Yayınlar Koleksiyonu / Scopus Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/11147/7148
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Article Linking RNA Methylation to Structure: A Biophysical Perspective(Wiley, 2026) Akgul, Bunyamin; Guler, Gunnur; Saglam, Buket; Akkus, Onur; Akcaoz-Alasar, AzimeRecent epitranscriptomic studies show that ribonucleic acids (RNAs) are coated with an array of chemical modifications that dictate their cellular fate. Genetic, biochemical, and genomic approaches have been employed to elucidate the molecular details of RNA methylation, one of the most prevalent types of RNA modifications with significant implications for health and disease. Various biochemical approaches have been developed to identify RNA methylations both at the global and nucleotide resolution levels. However, simpler detection methods are needed to assess the global methylation status of synthetic or cellular RNAs. Although significant progress has been made in elucidating the factors involved in writing, erasing, or reading methylated epitopes or structures, the impact of these methyl moieties on the secondary structure of RNAs or macromolecular interactions remains to be fully understood. Typically, biophysical approaches, such as Fourier transformed-infrared (FT-IR) spectroscopy, circular dichroism (CD), and Raman spectroscopy, have been used to study the structures and interactions of macromolecules, including DNA and proteins. Although RNAs harbor similar chemical modifications or structure-mediated functions, the number of RNA studies that employ biophysical approaches is scarce. In this viewpoint article, we present a biophysical perspective that links RNA methylation to structure and propose that FT-IR analyses can be employed to examine global changes in the abundance of cellular RNA m(6)A marks. Additionally, we discuss the potential applications of biophysical approaches that may be employed to gain insight into methylation-mediated changes in RNA structures.Article Salt Tolerance Potential of Selected Solanum Pennellii Introgression Lines: Unique Shoot and Root Responses(Wiley, 2025) Yildiz, Hatice Selale; Doganlar, Sami; Frary, AnneSalinity stress affects agricultural lands worldwide, causing serious yield losses. Investigation of the salinity response and tolerance mechanisms of crop plants and their wild relatives is important for developing tolerant varieties. In this study, three Solanum pennellii introgression lines (IL2-5, IL7-4-1, IL8-3), reported to be tolerant to abiotic stress, were investigated for their physiological and molecular responses to severe salinity (200 mM NaCl). The findings emphasized the variety of different responses that even highly genetically similar lines can have to stress. In IL2-5, a lack of significant root and shoot growth reduction due to salinity was associated with the up-regulation of vacuolar ion transporter genes (NHX1 and NHX3) and the lowest Na+ and Cl- accumulation in leaves, while beneficial K+ levels were preserved. In IL7-4-1, lateral root development was exceptionally strong compared to the other lines, with high Na+ and Cl- accumulation in leaves due to this unique root architecture. Despite this, the negative effects were lower on IL7-4-1's shoot growth than in IL8-3 and the control cultivar M82 due to effective reactive oxygen species management and increased superoxide gene expression. IL8-3's growth response was most similar to M82; however, it was better able to maintain beneficial K+ levels under salt stress. Overall, it was revealed that S. pennellii has multiple salt tolerance mechanisms associated with specific chromosomal segments and unique plant architecture. In addition to contributing to a better understanding of the mechanisms of salinity tolerance, these findings provide important information for increasing tolerance through targeted breeding.Article Storage Protein Allergen Sensitization Patterns in Children: Insights from Multiplex Microarray Profiling and Hierarchical Clustering(Wiley, 2025) Caka, Canan; Ozcivici, Engin; Karakus, Ceyda Oksel; Sekerel, Bulent EnisBackground Storage proteins (SPs), including 2S albumins, vicilins, and legumins, are key allergenic molecules (AMs) of peanuts, tree nuts (TNs), and sesame. Their structural stability contributes to allergenicity and sensitization. This study explored SP AM clustering patterns and evaluated the test performance of multiplex microarray (MM) testing in a pediatric cohort. Methods We retrospectively analyzed 350 children (median age: 3.7 years) with detectable SP sensitizations (>= 0.1 kU(A)/L) using the ALEX(2) MM platform. Sensitization interrelationships were analyzed using correlation heatmaps, hierarchical clustering (HC), dimensionality reduction, and feature elimination. Predictive utility was assessed through ROC curve analysis at different sensitization cut-offs (>0.1 and >0.3 kU(A)/L) and total IgE thresholds (>0, >20, and >50 kU/L). Results HC identified a broad SP cluster spanning peanuts, TNs, sesame, poppy seed, and buckwheat. Strong correlations and early HC linkages suggested extensive cross-sensitization (e.g., Ana o 3-Pis v 1 and Jug r 4-Cor a 9), alongside evidence of co-sensitization and molecular spreading. Unexpected clustering of structurally dissimilar peanut and pistachio AMs pointed to shared epitopes and/or cross-contamination. 2S albumins (Ara h 2, Cor a 14, Jug r 1, Ana o 3, and Ses i 1) were most predictive for clinical reactivity. Lower cut-offs and exclusion of patients with low total IgE improved test performance. Alpha-hairpinin (Pap s 2S albumin) showed potential as specific markers. Conclusions MM testing enables detailed SP sensitization profiling. Cluster-based interpretation may clarify cross- vs. co-sensitization, supporting informed clinical decisions. Use of recombinant AMs and IgE stratification may further enhance MM utility in food allergy diagnostics.Article Effect of Marination on the Formation of Polycyclic Aromatic Hydrocarbons in Grilled Vegetables(Wiley, 2025) Kacmaz Ozcetin, Sibel; Artok, LeventThe effect of marination on the formation of polycyclic aromatic hydrocarbons (PAH) in charcoal-grilled vegetables was studied. Various marinade ingredients, including apple cider vinegar, red grape vinegar, lemon juice, garlic powder, black pepper, and the food additive tert-butylhydroquinone (TBHQ) were applied to vegetable samples before charcoal grilling. The total phenolic content (TPC) and total antioxidant capacity (TAC) of each marinade ingredient were assessed for their contribution to PAH inhibition. A substantial decrease in PAH4 formation was observed in marinated vegetables. Red grape vinegar exhibited the strongest average inhibitory effect on total PAH4 formation (75%), followed by apple vinegar (68%), lemon juice (52%), garlic powder (34%), and black pepper (30%). Additionally, the TBHQ (67%) demonstrated a strong inhibitory effect, reducing total PAH4 formation by 67%. These findings offer valuable insights for reducing PAH levels in grilled vegetables and preventing their formation.Article Investigating the Effects of Functionalized Single Wall Carbon Nanotubes on the Cure Behavior of a Carbon/Epoxy Prepreg System by an Optimized Parameter Approach(Wiley, 2025) Oz, Murat; Uz, Yusuf Can; Tanoglu, Gamze; Tanoglu, Metin; Barisik, MuratCarbon/Epoxy composite materials are used in a wide range of applications due to their superior performance. However, their properties are strongly related to cross-linking reactions occurring during the curing process, and a prior estimation of curing parameters is the key to manufacturing the desired material. This study builds a mathematical model to solve the inverse kinetic problem based on differential scanning calorimetry data and later presents its use in curing experiments. The method derived (Gamze-Murat-Neslisah (GMN) approach) determines the pre-exponential and activation energy of the curing process. Later, an extended experimental study was performed. Functionalized single-wall carbon nanotubes (F-SWCNTs) were prepared by oxidizing their surface with carboxyl to enhance the dispersion of the nanoparticulates. The epoxy resin systems were modified with 0.05%, 0.1%, and 0.2% wt. F-SWCNTs, which were impregnated on carbon fibers (CFs). The curing behavior was studied, cure kinetic parameters were determined, and the thermal behavior was characterized. Differential scanning calorimetry (DSC) data sets for CF/epoxy prepregs containing F-SWCNTs were used for the verification of the proposed method. It was found that the GMN approach is in good agreement with the experimentally measured data for all kinetic parameters. The addition of F-SWCNTs increased the material's curing efficiency as the CNTs enhanced heat transport in composites, reducing the activation energy. The results obtained from the GMN algorithm were also found in good agreement with the well-known Kissinger-Akahira-Sunose (KAS) and Kissinger methods, while the current GMN method revealed itself as an accurate algorithm to obtain the activation energy.Article Citation - WoS: 5Citation - Scopus: 5Magnetically Controllable and Degradable Milliscale Swimmers as Intraocular Drug Implants(Wiley, 2025) Yildiz, E.; Bozuyuk, U.; Yildiz, E.; Wang, F.; Han, M.; Karacakol, A.C.; Sitti, M.Intraocular drug implants are increasingly used for retinal treatments, such as age-related macular degeneration and diabetic macular edema, due to the rapidly aging global population. Although these therapies show promise in arresting disease progression and improving vision, intraocular implant-based therapies can cause unexpected complications that require further surgery due to implant dislocation or uncontrolled drug release. These frequent complications of intraocular drug implants can be overcome using magnetically controllable degradable milliscale swimmers (MDMS) with a double-helix body morphology. A biodegradable hydrogel, polyethylene glycol diacrylate, is employed as the primary 3D printing material of MDMS, and it is magnetized by decorating it with biocompatible polydopamine-encapsulated iron-platinum nanoparticles. MDMS have comparable dimensions to commercial intraocular implants that achieve translational motions in both aqueous and vitreous bodies. They can be imaged in real-time using optical coherence tomography, ultrasound, and photoacoustic imaging. Thanks to their biodegradable hydrogel-based structure, they can be loaded with anti-inflammatory drug molecules and release the medications without disrupting retinal epithelial viability and barrier function, and decrease proinflammatory cytokine release significantly. These magnetically controllable swimmers, which degrade in a couple of months, can be used for less invasive and more precise intraocular drug delivery compared to commercial intraocular drug implants. © 2025 The Author(s). Advanced Science published by Wiley-VCH GmbH.Article Citation - Scopus: 1Transforming Crete's Sustainable Energy Landscape: a Modular Energy Island Approach(Wiley, 2025) Mendez-Morales, Mariela; Karipoglu, Fatih; Ivankovic, Marin; Lukic, Tamara; Rebelo, CarlosThe present paper investigates the conceptual design of a floating offshore renewable energy system-an energy island-developed to provide a sustainable long-term solution to support and expedite the transition toward renewable energy sources (RESs) as a case study in Crete Island, Greece. The optimal site selection in Crete's coastal waters was detected by carefully evaluating the potential for wind, solar, and wave energy alongside environmental and social considerations. Later, the current electricity demand was analyzed, leading to the identification of suitable technologies for renewable energy harvesting and the conceptualization of a floating structure. The findings of this research emphasize the viability of integrating diverse energy sources as a pivotal step for Crete Island to advance toward energy independence and environmental sustainability. Crete's abundant wind and solar resources underscore its capacity to host innovative projects, warranting further exploration into energy surplus storage and export.Article Citation - WoS: 3Citation - Scopus: 3Performance Improvement of Carbon Fiber-Reinforced Abs Composites by Introducing Fullerene Nanoparticles(Wiley, 2025) Akar, Alinda Oyku; Yildiz, Umit Hakan; Tirkes, Seha; Tayfun, Umit; Hacivelioglu, FerdaRecently, polymer composites have been extensively researched in industrial fields such as electrical conductance, ohmic heating, electromagnetic shielding and electrostatic discharge, particularly in engineering polymers reinforced with carbonaceous additions. Herein, fullerene (C60) and short carbon fiber (CF) were incorporated with acrylonitrile-butadiene-styrene copolymer (ABS) using melt-compounding followed by an injection-molding process. Composite samples were produced with contents of 20 wt% of CF besides 0.1, 0.5 and 1.0 wt% of C60. Tensile, impact, hardness and wear tests, conductive atomic force microscopy, dynamic mechanical analysis, thermogravimetric analysis, melt flow index tests and scanning electron microscopy (SEM) were performed to characterize mechanical, electrical, thermomechanical, thermal, melt-flow and structural behaviors of ABS-based composites involving CF and C60. Based on the mechanical test findings obtained for the developed composites, comprising tensile and impact test results, C60 additions contributed to a significant rise in tensile strength and impact resistance of CF-reinforced ABS composites, with a 20% increase in tensile resistance being achieved by introduction C60 into the ABS/CF structure. C60 addition enhanced efficiency by 50% in terms of tensile modulus. Electrical conductivity measurements confirmed that C60 nanoparticles and CF exhibited a synergy. The optimum synergistic ratio of C60/CF was obtained as 0.5/20. The conductive path in the ABS/CF composite system was established by incorporating C60 with different loading amounts. SEM micrographs of composites demonstrated that C60 nanoparticles were dispersed homogeneously into the ABS matrix involving lower amounts of C60. (c) 2025 The Author(s). Polymer International published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.Article Citation - WoS: 1Citation - Scopus: 1Hn1 Functions in Protein Synthesis Regulation Via Mtor-Rps6 Axis and Maintains Nucleolar Integrity(Wiley, 2025) Ozduman, Guelseren; Javed, Aadil; Alasar, Azime Akcaoz; Akgul, Buenyamin; Korkmaz, Kemal SamiHaematological and Neurological Expressed 1 (HN1) is an oncogene for various cancers and previously has been linked with centrosome clustering and cell cycle pathways. Moreover, HN1 has recently been reported to activate mTOR signalling, which is the regulator of ribosome biogenesis and maintenance. We explored the role of HN1 in mTOR signalling through various gain- and loss-of-function experiments using biochemical approaches in different cell lines. We demonstrated for the first time that HN1 is required for nucleolar organiser region (NOR) integrity and function. Immunoprecipitation-based association and colocalization studies demonstrated that HN1 is an important component of the mTOR-RPS6 axis, and its depletion results with reduced mRNA translation in mammalian cancer cell lines. This study also demonstrated that the depletion of HN1 leads to the irregular distribution of nucleolar structures, potentially leading to cell cycle deregulation as reported previously. Accordingly, components of the translation machinery aggregate with a distinct speckled pattern, lose their essential interactions and ultimately impair mRNA translation efficiency when the HN1 is depleted. These results suggest that HN1 is an essential component of the nucleolus, required for ribosome biogenesis as well as global mRNA translation.Article Secrecy performance of full-duplex space-air integrated networks in the presence of active/passive eavesdropper, and friendly jammer(Wiley, 2024) Buyuksar, Ayse Betul; Erdoğan, Eylem; Altunbas, IbrahimIn this paper, a full-duplex (FD) space-air ground integrated network (SAGIN) system with passive and active eavesdroppers (PE/AE) and a friendly jammer (FJ) is investigated. The shadowing side information (SSI)-based unmanned aerial vehicle relay node (URN) selection strategy is considered to improve signal-to-interference plus noise power ratio (SINR) at the ground destination unit. To quantify the secrecy performance of the considered scenario, outage probability (OP), interception probability (IP), and transmission secrecy outage probability (TSOP) are investigated in the presence of FJ and PE/AE. The results have shown that aerial AE is an important threat since it can severely degrade the OP of the main transmission link. Furthermore, the FJ can decrease the IP of the eavesdropper by causing interference with the cost of power consumption of URNs. Simulations are performed to verify the theoretical findings.