WoS İndeksli Yayınlar Koleksiyonu / WoS Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/11147/7150
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Article FTIR Spectroscopy Coupled With Chemometrics for Evaluating Functional Food Efficacy in an in Vitro Model of Iron Deficiency Anemia(Elsevier Science Ltd, 2026) Dalyan, Eda; Cavdaroglu, Cagri; Ozen, Banu; Gulec, SukruVibrational spectroscopy offers a rapid, cost-effective approach for studying biological systems. This study employs Fourier Transform Infrared (FTIR) spectroscopy, combined with Soft Independent Modeling of Class Analogy (SIMCA), to evaluate treatment outcomes for iron deficiency anemia (IDA). The model was built using spectra from healthy and anemic cells, then validated with cells treated with commonly used iron supplements. In calibration, 9 of 10 control and all IDA samples were correctly classified; 14 of 15 validation samples were identified as healthy. The model was applied to cells treated with protein-iron complexes. All samples treated with a 60:1 protein-iron ratio matched the healthy group, while 3 of 4 treated with a 10:1 ratio matched the IDA group. These results were further supported by iron-regulated gene expression of transferrin receptor (TFR) and (Ankyrin Repeat Domain 37) ANKRD37. FTIR coupled with chemometrics enables rapid assessment of functional effects and shows potential for screening functional ingredients in anemia-targeted food products.Article Alterations in Secondary Lipids Are Associated with Neuroinflammation in the Brain of Neu1-Deficient Mice(Springer, 2026) Ada, Ebru; Seyrantepe, VolkanNeu1 (lysosomal sialidase 1) is essential for removing sialic acid from oligosaccharides and glycoconjugates. Neu1 deficiency impairs lysosomal digestion, leading to sialidosis and sialoglycoprotein accumulation. It also increases lipids, including gangliosides GM3, GD3, GM4, and LM1, in the kidney, liver, and spleen. Neu1-/- mice display symptoms resembling Type II sialidosis, including enlarged spleen and liver, kidney issues, neurological problems, spinal defects, and oligosaccharide buildup. The study examined secondary lipid alterations and inflammation in the cortex and cerebellum of these mice. Lipidomic, molecular, and immunohistochemical analyses of tissues from 2 and 5 M Neu1-/- mice revealed reduced levels of lipids, including PC, PE, PS, and CL, along with increased pro-inflammatory cytokines and loss of oligodendrocytes and neurons. Signs of astrogliosis and microgliosis emerged in specific brain regions. These results indicate that reduced levels of glycerophospholipids could serve as an indicator of inflammation in sialidosis mice. Future research should investigate therapies targeting these lipid changes, as modulating glycerophospholipids might slow disease progression in sialidosis patients.Article Application of 3D Cell Culture Techniques in Nanotoxicology: How Far Are We(Springer, 2026) Shakeri, Raheleh; Mirjalili, Seyedeh Zohreh; Karakus, Ceyda Oksel; Safavi, MalihehInvestigation of toxicological profile and possible side effects of engineered nanomaterials (ENMs) is of high importance. Historically, two-dimensional (2D) cell culture was used to study the toxicity of the ENMs, but due to their inability to simulate in vivo cell behavior, three-dimensional (3D) cell culture systems have been developed. Nanotoxicity studies initiate with in vitro experiments and continue with in vivo studies, which are very challenging and sometimes accompanied by conflicting data due to the in vitro-in vivo gap. Thus, scientists are turning their attention to microfabrication techniques and engineered systems "called organ-on-a-chips", which act as an intermediate between in vivo and in vitro systems. The present account tries to review the classical study models and suitably cover the emerging 3D culture models including scaffold-free and scaffold-based 3D cell cultures, 3D co-culture with direct contact and without cell-cell contact methods as well as microfluidic-based tissue chips and organoids. Overall, this review aims to give readers a better insight about the ENMs' toxicology and fill the gaps between the knowledge and practical techniques. Hopefully, the presented information will resolve the issues of 2D in vitro cultures and display the clinically relevant responses to the concerns of therapeutic ENMs.Article Mass Spectrometric Profiling Reveals Alterations in N-Glycans and O-Glycans in Tay-Sachs Disease Under Autophagy-Induced Conditions(Springer, 2025) Can, Melike; Basirli, Hande; Jin, Chunsheng; Karlsson, Niclas G.; Bojar, Daniel; Seyrantepe, VolkanTay-Sachs disease is a rare neurodegenerative disorder caused by mutations in the HEXA gene. The HEXA gene encodes the alpha-subunit of the enzyme beta-hexosaminidase A, which degrades GM2 ganglioside. Previously, we identified impaired autophagy in the brains of a mouse model of Tay-Sachs disease, which exhibited neuropathological and clinical abnormalities. Moreover, we demonstrated autophagosome clearance in Tay-Sachs cells under lithium-induced conditions. Here, we further aimed to evaluate N- and O-glycan changes in these cells and examine whether glycan alterations are linked to ER stress. The profiles of N- and O-glycans were analyzed using LC-MS/MS in fibroblasts and neuroglial cells from 5-month-old Hexa-/-Neu3-/- mice and neuroglial cells from Tay-Sachs patients under lithium induction and nutrient deprivation. The expression levels of ER stress-related markers were assessed using qRT-PCR and Western blot analyses. We demonstrated higher levels of high mannose and lower levels of complex types of N-glycans, along with increased O-glycan levels in Tay-Sachs cells. Compared to control groups, we observed upregulated expression of endoplasmic reticulum (ER) stress-related markers, CHOP and ATF-6, in Tay-Sachs cells. Our study demonstrated that autophagy induction causes the degradation of accumulated high-mannose N-glycans and O-glycans, which is associated with the downregulation of ER stress-related genes in Tay-Sachs cells. Our study is the first to show this phenomenon in Tay-Sachs cells and suggests the presence of ER stress-mediated autophagy. Therefore, targeting glycans through autophagy induction could offer therapeutic benefits to patients with Tay-Sachs disease in future studies.Article Chloroaluminum Phthalocyanine Loaded Bovine Serum Albumin Nanoparticles as a Dual-Functional Nanoplatform for Sono-Photodynamic Cancer Therapy(Elsevier, 2026) Akyol-Karpuzcu, Cansu; Nartas, Eylem Doga; Calibasi-Kocal, Gizem; Akdogan, YasarChloroaluminum phthalocyanine (ClAlPc) loaded bovine serum albumin (BSA) nanoparticles (NPs) were synthesized as a dual-functional platform for photodynamic and sonodynamic therapies (PDT and SDT). ClAlPc loading did not disturb the morphology of the BSA NPs. Their spherical structure, with a size around 200 nm, was preserved upon ClAlPc loading (1 %w/w). Singlet oxygen productions in the presence of ClAlPc loaded BSA NPs or free ClAlPc were determined by ultraviolet absorption (UV-vis) spectroscopy and electron paramagnetic resonance (EPR) spectroscopy. While a slower rate of singlet oxygen formation rate after both PDT and SDT was detected by UV-vis measurements in the presence of ClAlPc loaded BSA NPs, EPR results showed a similar rate of singlet oxygen formation for both ClAlPc loaded BSA NPs and free ClAlPc. Confocal microscopy confirmed the efficient cellular uptake and perinuclear localization of the ClAlPc loaded BSA NPs in HCT-116 cancer cells. In vitro cytotoxicity studies demonstrated a dose and time dependent photo-and sonotoxic effects in the presence of ClAlPc loaded BSA. In particular, simultaneous application of light and ultrasound as sono-photodynamic therapy (SPDT) resulted in 15 % cell viability in the presence of ClAlPc loaded BSA NPs, which is much lower than individual PDT and SDT results, confirming the effect of the combination therapy on cell viability. In comparison, free ClAlPc reduced cell viability to 27 %. These findings suggest that ClAlPc loaded BSA NPs is a promising "one-for-two" nanoplatform for combined cancer therapy to reduce the limitations of both methods.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 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.Article A Simplified Molecular Imprinting Strategy Through Electrospinning of Polyacrylonitrile for Thin Film Microextraction of Selected Pesticides(Elsevier B.V., 2026) Şahin, A.; Akpinar, Y.; Yildirim, E.; Eroǧlu, A.E.; Boyaci, E.Molecularly imprinted polymers (MIPs) have been extensively used as selective extractive phases for sample preparation because of their analyte-selective binding sites. However, MIP preparation requires optimized monomer-template interactions and long polymerization reactions. In this study, a novel and simple method of MIP preparation was proposed based on electrospinning. Instead of preparing analyte-monomer complexes before polymerization, model analytes (trifluralin and carbaryl) were directly dissolved in a polyacrylonitrile (PAN) solution, then electrospun into nanofibrous mats. This allowed for a means of preparation of highly crystalline, template-imprinted nanostructures with minimal synthetic complexity. Following the characterization studies for the new material, the extraction properties of the imprinted and nonimprinted electrospun mats were investigated in thin film microextraction (TFME) studies by extracting trifluralin and carbaryl from water samples, followed by gas chromatography-mass spectrometry (GC–MS) analysis. The optimization results showed that samplers containing 10.0 mg of MIP sorbents made by electrospinning of a solution containing 5.0 mg of template in 1.0 mL of PAN solution resulted in approximately 4 and 7 times enhanced extraction recoveries for carbaryl and trifluralin compared to samplers made of non-imprinted bulk PAN. Moreover, the cross-reactivity testing performed with non-template analytes (malathion and diazinon) suggested a more specific extraction towards trifluralin compared to carbaryl. The proposed new technique was also validated using computational methodology, which supported the experimental finding about higher selectivity towards trifluralin. This may signify a probability for structural orientation of partially charged trifluralin under an electrical field in electrospun PAN creating favorable extraction sites. © 2025 Elsevier B.V.Article Enhanced Osteoconductive Properties of Quince Seed Hydrocolloid-Based Composite Scaffolds Enriched With Bioactive Glass for Bone Tissue Engineering(Wiley-VCH Verlag GmbH, 2025) Yilmaz-Dagdeviren, Hilal Deniz; Zheng, Kai; Boccaccini, Aldo Roberto; Arslan Yildiz, AhuBioactive composite scaffolds enhance osteoconduction and mineralization, offering potential for bone regeneration. In this study, polysaccharide-based Quince Seed Hydrocolloid (QSH) was combined with Gelatin (Gel), mesoporous bioactive glass nanoparticles (MBGNs), and 45S5 bioactive glass (BG) to fabricate osteoconductive scaffolds. QSH/Gel/BG and QSH/Gel/MBGN composites were characterized for chemical composition, mechanical behavior, and in vitro bioactivity. FTIR and SEM-elemental mapping confirmed homogeneous bioactive glass incorporation. BET analysis revealed a >3-fold increase in surface area for MBGN-containing scaffolds compared to BG and pristine QSH/Gel samples, attributed to the nanoscale mesoporous structure of MBGNs. Swelling tests showed a hydrophilic nature in all scaffolds, with MBGN composites exhibiting the highest swelling ratio (2094 +/- 571%), nearly twice that of BG composites (1105 +/- 56%). Compression tests indicated similar elastic moduli for MBGN and BG containing scaffolds (2330 and 2140 Pa). Human osteosarcoma cell cultures (28 days) demonstrated high viability (>70%) and osteoconductive response in all composites. Alizarin Red staining and SEM mapping revealed greater mineral accumulation in MBGN-containing scaffolds (Ca/P: 2.53). Overall, both composites supported a 3D osteoconductive microenvironment, while MBGN scaffolds exhibited superior long-term cell viability and mineralization potential, emphasizing their suitability for bone tissue engineering applications.Article Geogenic Determinants of Indoor Radon Exposure in Izmir (West Türkiye)(Pergamon-Elsevier Science Ltd, 2026) Alkan, Turkan; Simsek, Celalettin; Sac, Murat; Uzelli, Taygun; Taskin, NurcihanRadon, a naturally occurring product of uranium decay, is the second leading cause of lung cancer. I(center dot)zmir Province in western T & uuml;rkiye, situated within the Aegean extensional regime, comprises complex fault-bounded basins that favor indoor radon accumulation. This study evaluates the spatial variability and geogenic controls of indoor radon to delineate radon-prone zones with public-health relevance. Indoor radon was measured in 79 dwellings distributed across major lithologies and structural settings; detectors were deployed in basements to capture soil-gas infiltration. Concentrations ranged from 12 to 366.5 Bq/m3 (mean 118 Bq/m3), exceeding the national average of 81 Bq/m3; 32 % of sites surpassed the EPA action level of 148 Bq/m3. Highest values cluster in Bornova, Buca, and Kemalpas, a, coincident with fault-controlled sedimentary basins and permeable units. Spatial mapping highlights the dominant influence of lithology and fault proximity on radon distribution and underscores the limitations of uniform, national-scale mitigation policies. We advocate targeted, geology-aware health policies and urban-planning measures for monitoring and mitigation in geogenically vulnerable districts. These findings contribute to medical geology by providing region-specific evidence of radon risk in one of T & uuml;rkiye's most seismically active metropolitan areas. These outputs provide decision-ready evidence for monitoring, mitigation, and building-code updates in seismically active metropolitan settings.