PubMed İndeksli Yayınlar Koleksiyonu / PubMed Indexed Publications Collection

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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, Sukru
    Vibrational 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
    Application of 3D Cell Culture Techniques in Nanotoxicology: How Far Are We
    (Springer, 2026) Shakeri, Raheleh; Mirjalili, Seyedeh Zohreh; Karakus, Ceyda Oksel; Safavi, Maliheh
    Investigation 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
    Hydrogeochemical Assessment and Health Risks of Groundwater in Sahand Volcanic Foreland (NW Iran): Arsenic Speciation and Heavy Metal Risk Indicators
    (Academic Press Inc Elsevier Science, 2026) Ghayurdoost, Farhad; Zarghami, Mahdi; Sadeghfam, Sina; Jabraili-Andaryan, Nasser; Nikmaram, Sara; Baba, Alper; Mosaferi, Mohammad
    Due to the toxic nature of arsenic (As) and its elevated concentrations in many water resources, numerous studies have focused on understanding its origin, distribution, and impacts. This study aimed to identify the dominant As species in groundwater of the Sahand Volcanic Foothills, assess water quality indices, and examine heavy metal (HM) concentrations to address rising concerns about groundwater contamination. A total of 21 groundwater samples were collected and analyzed in accordance with world health organization (WHO) guidelines. Although most samples fell within acceptable ranges, several (notably S10, S20, and S21) exhibited elevated levels of total dissolved solids (TDS), electrical conductivity (EC), and HMs, particularly iron (Fe) and As. Hydrochemical assessments using Piper, Gibbs, Stiff, and Schoeller diagrams indicated that geochemical processes resulting from rock dissolution were the main factors controlling groundwater chemistry, with limited influence from anthropogenic pollution. According to the groundwater quality index (GWQI), most samples were categorized as "good" to "excellent," though some areas ranged from "moderate" to "very poor." HM pollution indices revealed that As concentrations exceeded permissible limits. Health risk assessments further showed that both oral and dermal exposure posed significant carcinogenic and non-carcinogenic risks, especially for children. Speciation analysis indicated that arsenate (As V) was the dominant form of As, consistent with oxidizing aquifer conditions, and is less biologically hazardous than arsenite (As III). The study highlights the necessity of continuous groundwater monitoring, effective pollution source management, and implementation of protective regulations to mitigate environmental and health risks in the region.
  • Article
    Notum1a Inhibition Promotes Neurogenesis in the Adult Zebrafish Brain
    (Nature Portfolio, 2025) Kocagoz, Yigit; Erdogan, Nuray Sogunmez; Ozdinc, Sevval; Ipekgil, Dogac; Katkat, Esra; Ozhan, Gunes
    Notum is a carboxylesterase enzyme that modulates extracellular signaling by hydrolyzing palmitoleoyl residues from proteins, thereby influencing key pathways involved in cell differentiation, survival, and proliferation. While notum1 expression has been identified in the brain, its role in adult neurogenesis remains poorly understood. Using the adult zebrafish brain as a model system, we demonstrate that the notum1a homolog is broadly expressed across various brain cell types but is absent in undifferentiated radial glial cells. Pharmacological inhibition of Notum activity with the small molecule inhibitor ABC99 stimulates activation of radial glial cells, leading to increased neurogenesis. A BrdU pulse-chase assay confirms that ABC99-induced proliferation enhances the production of mature neurons. Despite Notum's established role in Wnt signaling, transcriptional analysis following ABC99 treatment reveals no sustained impact on Wnt pathway targets, suggesting that Notum may regulate neurogenesis through alternative mechanisms. Our findings highlight notum1a as a potential modulator of neural progenitor cell dynamics in the adult brain and suggest that targeting Notum could represent a novel therapeutic strategy for neurodegenerative conditions characterized by impaired neurogenesis.
  • Article
    Iron Oxide Nanocube Assembly on Silver Nanowire Templates to Enhance Magnetic Hyperthermia Performance
    (Royal Society of Chemistry, 2026) Arica, Tugce A.; Tiryaki, Ecem; Sadeghi, Ehsan; Mannir, Abubakar R.; Balci, Sinan; Pellegrino, Teresa
    Iron oxide nanocubes (IONCs) represent one of the benchmark magnetic nanoparticles able to most efficiently convert magnetic energy into heat for magnetic hyperthermia cancer treatment, and their heat losses can be further increased by controlling their assembly through the synthesis of ordered structures. However, achieving the alignment of nanoparticles with one-dimensional chain or columnar structures into long arrays to then study their magnetic heat losses still remains a significant challenge. This study exploits silver nanowires as high-surface-area anisotropic templates for the controlled chaining of IONCs. The surfaces of the IONCs were purposely functionalized with polyethyleneimine (IONCs@PEI) and interacted with silver nanowire (AgNW) surfaces via electrostatic attraction. Here, alternating current (AC) magnetometry was employed to compare the heating performance expressed as specific absorption rate values between individually coated IONCs@PEI and AgNWs@IONCs@PEI composites at various magnetic field strengths and frequencies. SAR values reveal that clustering of IONCs on AgNW surfaces improves the heating efficiency at an applied magnetic field strength of 24 kA m-1, regardless of the applied frequencies, with SAR values of AgNWs@IONCs@PEI composites outperforming those of individual IONCs@PEI. Moreover, dynamic hysteresis loops showed that the coercive field of AgNWs@IONCs@PEI increased significantly at 24 kA m-1, indicating the existence of strong magnetic dipolar interactions between nanoparticles. This study shows an innovative approach for guiding the orientation of magnetic nanoparticles using one-dimensional templates to enhance their heating performance.
  • Article
    Temporal Coherence of Single Photons Emitted by Hexagonal Boron Nitride Defects at Room Temperature
    (Amer Chemical Soc, 2026) Martinez-Pons, Juan Vidal; Kim, Sang Kyu; Behrens, Max; Izquierdo-Molina, Alejandro; Menendez Rua, Adolfo; Pacal, Serkan; Anton-Solanas, Carlos
    Color centers in hexagonal boron nitride (hBN) emerge as promising quantum light sources at room temperature, with potential applications in quantum communications, among others. The temporal coherence of emitted photons (i.e., their capacity to interfere and distribute photonic entanglement) is essential for many of these applications. Hence, it is crucial to study and determine the temporal coherence of this emission under different experimental conditions. In this work, we report the coherence time of the single photons emitted by an hBN defect in a nanocrystal at room temperature, measured via Michelson interferometry. The visibility of this interference vanishes when the temporal delay between the interferometer arms is a few hundred femtoseconds, highlighting that the phonon dephasing processes are 4 orders of magnitude faster than the spontaneous decay time of the emitter. We also analyze the single photon characteristics of the emission via correlation measurements, defect blinking dynamics, and its Debye-Waller factor. Our room temperature results highlight the presence of a strong electron-phonon coupling, suggesting the need to work at cryogenic temperatures to enable quantum photonic applications based on photon interference.
  • 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, Yasar
    Chloroaluminum 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, Azime
    Recent 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
    Investigation of Few-Layer Graphene-Ubiquitin Interactions with Optical Spectroscopy Techniques
    (MDPI, 2025) Gencay, Burcu; Guler, Gunnur
    Understanding the molecular mechanisms of protein-nanoparticle interactions is crucial for enabling the development of new applications in biomedicine and nanotechnology. Ubiquitin, an important and structurally small functional protein, plays a central role in numerous cellular processes. Therefore, in the current study, we focused on the few-layer graphene (FLG)-Ubiquitin complexes formed by exfoliating FLG structures using only water. Optical spectroscopic techniques (Raman, FT-IR, UV-Vis and circular dichroism) were employed to investigate these complexes on the molecular level. Overall, both CD and FT-IR data reveal that the formation of the FLG-Ubiquitin complexes occurred without inducing disordered structures in the protein. Based on the existence of a blue shift (hypsochromic shift) in the UV-Vis data, the presence of a single tyrosine and two phenylalanine residues in ubiquitin enables the detection of FLG-induced micro-environmental changes, particularly influencing the protein's beta-sheet and alpha-helix structures. The CD spectral results and CDPro quantitative estimations are in line with ATR FT-IR results, confirming the absence of disordered structure formation while altering the protein's chirality. UV-Vis and CD spectroscopy results revealed concentration-dependent trends consistent with FLG-protein interactions that preserve the overall protein structure. This study has potential applications in both academic research and practical usage, particularly in biomedicine and nanotechnology specifically for FLG.
  • Article
    The Effects of Lactobacillus and/or Bifidobacterium in Fermented Foods on Cognitive Health: A Systematic Review
    (Frontiers Media SA, 2025) Harsa, Hayriye Sebnem; Gonzalez Domenech, Carmen Maria; Prvulovic, Milica; Agirbasli, Zeynep; Bagherzadehsurbagh, Erfan; Simeunovic, Valentina; Pracer, Smilja
    Background: Psychobiotics are microorganisms that modulate brain function via the gut-brain axis and are increasingly studied for their cognitive benefits. Lactobacillus and Bifidobacterium species, widely present in fermented foods, are considered safe and may influence cognition by modulating neuroinflammation, neurotransmitters, and gut barrier integrity. This systematic review examined the effects of foods fermented with these species on cognitive performance in healthy adults and individuals with mild cognitive impairment. Methods: We conducted the systematic review following EFSA guidelines, Cochrane methodology, and a PROSPERO protocol, using CADIMA for study selection and data extraction. PubMed, Scopus, and Cochrane Library were searched (1 January 1970-31 August 2023) for human intervention and observational studies assessing cognitive outcomes after ingestion of foods fermented with Lactobacillus or Bifidobacterium. Eligible populations included healthy adults and individuals with mild cognitive impairment; studies involving disease were excluded. Screening, data extraction, and bias assessment followed Muka et al.'s 24-step guide using ROBINS and Cochrane/CADIMA frameworks. Evidence was synthesized narratively, while a non-systematic component examined food characteristics, potential mechanisms, and factors affecting bioavailability of bioactive constituents. Results: We included 21 studies (8 interventional, 13 observational). The majority of studies reported benefits, particularly in episodic memory, executive functions, and global cognition, but evidence was limited by inadequate controls, small sample sizes, short interventions, inconsistent domain assessment, and incomplete food characterization. Observational studies had larger populations and longer follow-ups but were limited by exposure assessment and depth of cognitive testing. Conclusion: Consumption of foods fermented with Lactobacillus and/or Bifidobacterium species may offer promising cognitive benefits. However, following EFSA's guidance on the substantiation of health claims, the current evidence is "neither convincing nor sufficient" to establish a causal relationship. Well-designed studies with thorough product characterization are needed to substantiate effects and support potential health claims.