PubMed İndeksli Yayınlar Koleksiyonu / PubMed Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/11147/7645
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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 Citation - WoS: 4Citation - Scopus: 3Unveiling Bone and Dental Regeneration Potential of Quince Seed Mucilage-Nanohydroxyapatite Scaffolds in Rabbit Mandibles(Wiley, 2025) Genc, Cigdem Cetin; Yilmaz-Dagdeviren, Hilal Deniz; Deniz, Yesim; Derkus, Burak; Degirmenci, Alpin; Arslan, Yavuz EmreDonor-side morbidity of autografting for maxillofacial region defect regeneration has directed attention to bioengineered scaffolds. Composite scaffolds that mimic the bone extracellular matrix (ECM) are the potential candidates for defect reconstruction. Herein, a plant-based regenerative hydrogel, quince seed mucilage (QSM), was enriched with the nanohydroxyapatite (nHAp) particles to construct composite scaffolds (QSM/nHAp). The emerging scaffold is able to induce cellular spheroid formation and regenerate the critical-sized bilateral mandibular defects in rabbits. The macroscopic observations, histochemical (HC) and immunohistochemical (IHC) stainings, mu-computer tomography (CT) scanning, quantitative real time-polymerase chain reaction (qRT-PCR) analyses, and scanning electron microscopy (SEM) imaging revealed that all QSM/nHAp scaffolds were swelled with host blood, filled the whole cavity, and sustained cellular infiltration without adverse reactions. The gradual biodegradation profile of the scaffolds improved bone regeneration by releasing nHAp particles from the scaffold. Strikingly, co-development of dental and bone regeneration was observed for all QSM/nHAp groups beginning after day 21. Moreover, QSM/nHAp scaffolds induced expression (> 2-fold) of bone and dental-related gene and protein expressions at the grafted area and sustained a proper platform for maxillofacial remodeling. Therefore, we strongly believe that such biocompatible plant-based constructs, compared with conventional medical devices used in maxillofacial surgery, could support and induce simultaneous bone and dental regeneration due to the intrinsic dynamics of the material.Article Phenotypically Plastic Drug-Resistant Chronic Myeloid Leukaemia Cell Line Displays Enhanced Cellular Dynamics in a Zebrafish Xenograft Model(Wiley, 2024) Baykal, Seda; Yuce, Zeynep; Ozhan, GunesUnderstanding the mechanisms by which cancer cells switch between different adaptive states and evade therapeutic interventions is essential for clinical management. In this study, the in vivo cellular dynamics of a new chronic myeloid leukaemia cell line displaying altered phenotype and resistance to tyrosine kinase inhibitors were investigated in correlation with their parental cells for invasiveness/metastasis, angiogenic potential and population kinetics. We showed that the cells exhibiting drug resistance and plastic phenotype possess an increased capacity for invasion compared to their parental cells, that exposure to imatinib mesylate has the potential to enhance cellular motility and that in a leukaemic cell population, even a minority of plastic cells exhibit improved migratory ability. Furthermore, we show that these plastic cells have angiogenic and extravasation potential. The present study provides significant insights into the cellular dynamics displayed by a TKI-resistant, phenotypically plastic CML cell line, using a zebrafish (Danio rerio) xenograft model.Article Citation - WoS: 4Citation - Scopus: 5Near-Infrared Emissive Super Penetrating Conjugated Polymer Dots for Intratumoral Imaging in 3d Tumor Spheroid Models(Wiley, 2024) Karabacak, Soner; Coban, Basak; Yildiz, Ahu Arslan; Yildiz, Umit HakanThis study describes the formation of single-chain polymer dots (Pdots) via ultrasonic emulsification of nonionic donor-acceptor-donor type (D-A-D) alkoxy thiophene-benzobisthiadiazole-based conjugated polymers (Poly BT) with amphiphilic cetyltrimethylammonium bromide (CTAB). The methodology yields Pdots with a high cationic surface charge (+56.5 mV +/- 9.5) and average hydrodynamic radius of 12 nm. Optical characterization reveals that these Pdots emit near-infrared (NIR) light at a maximum wavelength of 860 nm owing to their conjugated polymer backbone consisting of D-A-D monomers. Both colloidal and optical properties of these Pdots make them promising fluorescence emissive probes for bioimaging applications. The significant advantage of positively charged Pdots is demonstrated in diffusion-limited mediums such as tissues, utilizing human epithelial breast adenocarcinoma, ATCC HTB-22 (MCF-7), human bone marrow neuroblastoma, ATCC CRL-2266 (SH-SY5Y), and rat adrenal gland pheochromocytoma, CRL-1721 (PC-12) tumor spheroid models. Fluorescence microscopy analysis of tumor spheroids from MCF-7, SH-SY5Y, and PC-12 cell lines reveals the intensity profile of Pdots, confirming extensive penetration into the central regions of the models. Moreover, a comparison with mitochondria staining dye reveals an overlap between the regions stained by Pdots and the dye in all three tumor spheroid models. These results suggest that single-chain D-A-D type Pdots, cationized via CTAB, exhibit long-range mean free path of penetration (approximate to 1 mu m) in dense mediums and tumors. The single chain near infrared (NIR) emissive Pdots with high cationic surface charge enable penetration in dense medium such as tumor spheroids. Both colloidal and optical properties of Pdots make them promising fluorescent probe in bioimaging. imageReview Citation - WoS: 3Citation - Scopus: 4Long Non-Coding Rna-Mediated Modulation of Endoplasmic Reticulum Stress Under Pathological Conditions(Wiley, 2024) Ciftci, Yusuf Cem; Yurtsever, Yigit; Akgul, BunyaminEndoplasmic reticulum (ER) stress, which ensues from an overwhelming protein folding capacity, activates the unfolded protein response (UPR) in an effort to restore cellular homeostasis. As ER stress is associated with numerous diseases, it is highly important to delineate the molecular mechanisms governing the ER stress to gain insight into the disease pathology. Long non-coding RNAs, transcripts with a length of over 200 nucleotides that do not code for proteins, interact with proteins and nucleic acids, fine-tuning the UPR to restore ER homeostasis via various modes of actions. Dysregulation of specific lncRNAs is implicated in the progression of ER stress-related diseases, presenting these molecules as promising therapeutic targets. The comprehensive analysis underscores the importance of understanding the nuanced interplay between lncRNAs and ER stress for insights into disease mechanisms. Overall, this review consolidates current knowledge, identifies research gaps and offers a roadmap for future investigations into the multifaceted roles of lncRNAs in ER stress and associated diseases to shed light on their pivotal roles in the pathogenesis of related diseases.Article Citation - Scopus: 1Mitigating Thermal Stratification in Lakes/Reservoirs Through Wind-Powered Air Diffusers(Wiley, 2024) Hazar, Oguz; Elci, SebnemThermal stratification can cause various water quality issues in large water bodies. To address this, a new wind-powered artificial mixing system is designed and experimentally tested for various Savonius rotor combinations (three-stage and four-stage rotors). These turbines directly utilize wind energy to draw air into the water column for aeration, bypassing the need for electrical conversion. The rotor performances were tested in terms of power and torque coefficients. Additionally, these rotors were tested for artificial mixing efficiencies in a specially designed water tank that can mimic thermal stratification typically observed in an actual water supply reservoir. Among the rotors, the three-stage rotor with a 60 degrees phase shift was found to exhibit superior power and torque coefficients, achieving a power efficiency value of 0.14. As for the mixing efficiency, the four-stage rotor with a 45 degrees phase shift excelled in mixing efficiency, reaching 95%.Practitioner Points A new wind-powered artificial mixing system is designed and tested for various Savonius rotor combinations. While keeping the total rotor height constant, the three-stage Savonius rotor class shows superior performance against the four-stage Savonius rotor class in terms of power and torque efficiency. Apart from the rotor performance results, the four-stage Savonius rotors show greater artificial mixing efficiency than the three-stage Savonius rotors. Single-pump/diffuser artificial destratification system exhibits better mixing efficiency than multiple-pump/diffuser systems. A new wind-powered artificial mixing system is designed and tested for various Savonius rotor combinations. The three-stage 60 degrees phase shift Savonius rotor demonstrated the best performance of turbine efficiency. The four-stage Savonius rotor with a 45 degrees phase shift connected to a single-pump system achieved the highest destratification efficiency at 95%. imageReview Citation - WoS: 4Citation - Scopus: 4Unraveling the Intriguing Interplay: Exploring the Role of Lncrnas in Caspase-Independent Cell Death(Wiley, 2024) Ciftci, Yusuf Cem; Akgül, Bünyamin; Vatansever, Ipek Erdogan; Akgul, BuenyaminCell death plays a crucial role in various physiological and pathological processes. Until recently, programmed cell death was mainly attributed to caspase-dependent apoptosis. However, emerging evidence suggests that caspase-independent cell death (CICD) mechanisms also contribute significantly to cellular demise. We and others have reported and functionally characterized numerous long noncoding RNAs (lncRNAs) that modulate caspase-dependent apoptotic pathways potentially in a pathway-dependent manner. However, the interplay between lncRNAs and CICD pathways has not been comprehensively documented. One major reason for this is that most CICD pathways have been recently discovered with some being partially characterized at the molecular level. In this review, we discuss the emerging evidence that implicates specific lncRNAs in the regulation and execution of CICD. We summarize the diverse mechanisms through which lncRNAs modulate different forms of CICD, including ferroptosis, necroptosis, cuproptosis, and others. Furthermore, we highlight the intricate regulatory networks involving lncRNAs, protein-coding genes, and signaling pathways that orchestrate CICD in health and disease. Understanding the molecular mechanisms and functional implications of lncRNAs in CICD may unravel novel therapeutic targets and diagnostic tools for various diseases, paving the way for innovative strategies in disease management and personalized medicine.Article Citation - WoS: 6Epitranscriptomics M<sup>6</Sup>a Analyses Reveal Distinct M<sup>6</Sup>a Marks Under Tumor Necrosis Factor Α (tnf-Α) Apoptotic Conditions in Hela Cells(Wiley, 2024) Akçaöz Alasar, Azime; Tüncel, Özge; Sağlam, Buket; Gazaloğlu, Yasemin; Atbinek, Melis; Çağıral, Umut; Akgül, BünyaminTumor necrosis factor-alpha (TNF-alpha) is a ligand that induces both intrinsic and extrinsic apoptotic pathways in HeLa cells by modulating complex gene regulatory mechanisms. However, the full spectrum of TNF-alpha-modulated epitranscriptomic m(6)A marks is unknown. We employed a genomewide approach to examine the extent of m(6)A RNA modifications under TNF-alpha-modulated apoptotic conditions in HeLa cells. miCLIP-seq analyses revealed a plethora of m(6)A marks on 632 target mRNAs with an enrichment on 99 mRNAs associated with apoptosis. Interestingly, the m(6)A RNA modification patterns were quite different under cisplatin- and TNF-alpha-mediated apoptotic conditions. We then examined the abundance and translational efficiencies of several mRNAs under METTL3 knockdown and/or TNF-alpha treatment conditions. Our analyses showed changes in the translational efficiency of TP53INP1 mRNA based on the polysome profile analyses. Additionally, TP53INP1 protein amount was modulated by METTL3 knockdown upon TNF-alpha treatment but not CP treatment, suggesting the existence of a pathway-specific METTL3-TP53INP1 axis. Congruently, METLL3 knockdown sensitized HeLa cells to TNF-alpha-mediated apoptosis, which was also validated in a zebrafish larval xenograft model. These results suggest that apoptotic pathway-specific m(6)A methylation marks exist in cells and TNF-alpha-METTL3-TP53INP1 axis modulates TNF-alpha-mediated apoptosis in HeLa cells.Article Citation - WoS: 14Citation - Scopus: 14Comparative Membrane Lipidomics of Hepatocellular Carcinoma Cells Reveals Diacylglycerol and Ceramide as Key Regulators of Wnt/Β-catenin Signaling and Tumor Growth(Wiley, 2023) Heger, Guillaume; Azbazdar, Yağmur; Demirci, Yeliz; İpekgil, Doğaç; Karabiçici, Mustafa; Özhan, GüneşHepatocellular carcinoma (HCC) is largely associated with aberrant activation of Wnt/beta-catenin signaling. Nevertheless, how membrane lipid composition is altered in HCC cells with abnormal Wnt signaling remains elusive. Here, by exploiting comprehensive lipidome profiling, we unravel the membrane lipid composition of six different HCC cell lines with mutations in components of Wnt/beta-catenin signaling, leading to differences in their endogenous signaling activity. Among the differentially regulated lipids are diacylglycerol (DAG) and ceramide, which were downregulated at the membrane of HCC cells after Wnt3a treatment. DAG and ceramide enhanced Wnt/b-catenin signaling by inducing caveolin-mediated endocytosis of the canonical Wnt-receptor complex, while their depletion suppressed the signaling activity along with a reduction of caveolin-mediated endocytosis in SNU475 and HepG2 cells. Moreover, depletion of DAG and ceramide significantly impeded the proliferation, tumor growth, and in vivo migration capacity of SNU475 and HepG2 cells. This study, by pioneering plasma membrane lipidome profiling in HCC cells, exhibits the remarkable potential of lipids to correct dysregulated signaling pathways in cancer and stop abnormal tumor growth.Article Citation - WoS: 7Citation - Scopus: 8Bioinspired Multi-Layer Biopolymer-Based Dental Implant Coating for Enhanced Osseointegration(Wiley, 2023) Üzülmez, Betül; Demirsoy, Zeynep; Can, Özge; Gülseren, GulcihanThe major drawbacks of metal-based implants are weak osseointegration and post-operational infections. These limitations restrict the long-term use of implants that may cause severe tissue damage and replacement of the implant. Recent strategies to enhance the osseointegration process require an elaborate fabrication process and suffer from post-operative complications. To address the current challenges taking inspiration from the extracellular matrix (ECM), the current study is designed to establish enhanced osseointegration with lowered risk of infection. Natural biopolymer pectin, peptide amphiphiles, and enzyme-mimicking fullerene moieties are governed to present an ECM-like environment around the implant surfaces. This multifunctional approach promotes osseointegration via inducing biomineralization and osteoblast differentiation. Application of the biopolymer-based composite to the metal surfaces significantly enhances cellular attachment, supports the mineral deposition, and upregulates osteoblast-specific gene expression. In addition to the osteoinductive properties of the constructed layers, the inherent antimicrobial properties of multilayer coating are also used to prevent infection possibility. The reported biopolymer-artificial enzyme composite demonstrates antimicrobial activity against Escherichia coli and Bacillus subtilis as a multifunctional surface coating.