PubMed İndeksli Yayınlar Koleksiyonu / PubMed Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/11147/7645
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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, GunesNotum 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.Correction Database Covering the Prayer Movements Which Were Not Available Previously (Vol 10, 276, 2023)(Nature Portfolio, 2025) Mihcin, Senay; Sahin, Ahmet Mert; Yilmaz, Mehmet; Alpkaya, Alican Tuncay; Tuna, Merve; Akdeniz, Sevinc; Sahin, SerapArticle Integrated Spectroscopic and Morphological Analyses Reveal Cellular Shifts in Gene-Silenced Melanoma CSCs(Nature Portfolio, 2025) Ozdil, Berrin; Guler, Gunnur; Ataman, Evren; Aktug, HuseyinIntratumoral heterogeneity remains a major barrier to durable cancer therapies, largely driven by the persistence of cancer stem cells (CSCs). In this study, we employed an integrated, multi-scale approach to investigate how melanoma CSCs respond to siRNA-mediated silencing of three key regulatory genes: KLF4, SHH, and HIF1 alpha. Using a combination of morphological, molecular, spectroscopic, and elemental analyses, we explored structural and biochemical consequences of gene knockdown. Gene silencing resulted in significant changes in cell shape and size, reduced F-actin organization, and decreased PFN1 expression, indicating a loss of stem-like properties. ATR-FTIR spectroscopy revealed shifts in biomolecular composition, notably a reduction in amide III intensity and an increase in lipid ester content. SEM-EDS point-based elemental analysis revealed SEM-EDS point-based elemental analysis revealed relative differences in carbon and nitrogen levels between selected central and peripheral regions of silenced and control cells, at the micron-scale working depth, reflecting broader elemental distribution trends rather than precise subcellular compartmentalization. XPS analysis further confirmed these differences, providing additional insights into the elemental composition of the cellular surface. The integration of FTIR spectroscopy into this study highlights the potential of infrared spectroscopy as a powerful tool in cancer research. These findings demonstrate that targeting critical regulatory pathways induces cytoskeletal and biochemical remodelling in melanoma CSCs, offering a multi-dimensional perspective on cellular plasticity.Article Citation - WoS: 2Citation - Scopus: 2Vibrational Spectroscopy Unveils Distinct Cell Cycle Features of Cancer Stem Cells in Melanoma(Nature Portfolio, 2025) Uslu, Bensu Ruya; Ozdil, Berrin; Tarhan, Enver; Ozcelik, Serdar; Aktug, Huseyin; Guler, GunnurCancer stem cells (CSCs) play a central role in melanoma growth, resistance to treatment, and relapse, however, their dynamic regulatory behavior remains poorly understood. Vibrational spectroscopy offers a unique, label-free approach to investigate cellular heterogeneity at the molecular level. Here, we explored the biochemical and regulatory dynamics of CSCs identified by using a time-course design, integrating infrared and Raman spectroscopies with cell cycle analysis and immunocytochemistry targeting the checkpoint proteins p16 and p21. CSCs, non-cancer stem cells (NCSCs), and bulk CHL-1 melanoma cells were monitored at 11, 24, 48, and 72 h. CSCs showed a steady S-phase with an early rise in p16 followed by a subsequent increase in p21 expression, indicating a dynamic state of cell cycle checkpoints. In contrast, NCSCs and CHL-1 cells showed more transient p16/p21 expression and CHL-1 exhibited a marked p16 increase at 24 h. Spectroscopic analysis revealed that CSCs exhibited distinct vibrational profiles, predominantly in the nucleic acid-, protein- and lipid-associated regions. These differences were further supported by principal component and hierarchical clustering analyses, which consistently distinguished CSCs from NCSCs. Our findings underline the potential of vibrational spectroscopy to sensitively detect CSC-specific regulatory patterns and support its use in detecting new therapeutic targets in melanoma.Article Citation - WoS: 10Citation - Scopus: 9Quantifying Hydrogen Bonding Using Electrically Tunable Nanoconfined Water(Nature Portfolio, 2025) Wang, Ziwei; Bhattacharya, Anupam; Yagmurcukardes, Mehmet; Kravets, Vasyl; Diaz-Nunez, Pablo; Mullan, Ciaran; Mishchenko, ArtemHydrogen bonding plays a crucial role in biology and technology, yet it remains poorly understood and quantified despite its fundamental importance. Traditional models, which describe hydrogen bonds as electrostatic interactions between electropositive hydrogen and electronegative acceptors, fail to quantitatively capture bond strength, directionality, or cooperativity, and cannot predict the properties of complex hydrogen-bonded materials. Here, we introduce a concept of hydrogen bonds as elastic dipoles in an electric field, which captures a wide range of hydrogen bonding phenomena in various water systems. Using gypsum, a hydrogen bond heterostructure with two-dimensional structural crystalline water, we calibrate the hydrogen bond strength through an externally applied electric field. We show that our approach quantifies the strength of hydrogen bonds directly from spectroscopic measurements and reproduces a wide range of key properties of confined water reported in the literature. Using only the stretching vibration frequency of confined water, we can predict hydrogen bond strength, local electric field, O-H bond length, and dipole moment. Our work also introduces hydrogen bond heterostructures - a class of electrically and chemically tunable materials that offer stronger, more directional bonding compared to van der Waals heterostructures, with potential applications in areas such as catalysis, separation, and energy storage.Article Citation - WoS: 7Citation - Scopus: 7Comparative Analysis of Volume Change Behavior of Expansive Road Subgrades Stabilized With Waste Paper Sludge(Nature Portfolio, 2024) Tanyildizi, Muhammed; Goekalp, Islam; Zeybek, Abduelhakim; Uz, Volkan EmreExpansive soils have a high tendency for volume change in case of fluctuations in moisture content, potentially causing significant damage to light structures, particularly road pavements. This paper investigates the influence of waste paper sludge (\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\:WPS$$\end{document}) as an alternative sustainable stabilizer on the volume change behavior of expansive road subgrade soils of different origins. For this purpose, \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\:WPS$$\end{document} was added to the expansive soils at ratios of 3%, 6%, 9%, 12%, and 15% by dry weight of the soils. A series of Atterberg's limit, swelling, shrinkage, compaction, and consolidation tests were performed on pure soils and soil specimens with \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\:WPS$$\end{document} to attain a comprehensive understanding of the role that \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\:WPS$$\end{document} plays in the volume change behavior of expansive soils. The experimental test results showed that the addition of \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\:WPS\:$$\end{document} led to a considerable decrease in the plasticity and swell-shrink potentials of subgrade soils. The consolidation settlement of expansive road subgrades was also reduced to some extent with \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\:WPS$$\end{document}. Moreover, the statistical analysis of the test data indicated a significant relationship among different swelling-shrinkage parameters. The experimental results presented here suggest that the \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\:WPS$$\end{document} may be a cost-effective, environmentally friendly, and sustainable stabilizer to reduce the volume change sensitivity of expansive road subgrade soils.Article Citation - WoS: 2Citation - Scopus: 1Gliflozins, Sucrose and Flavonoids Are Allosteric Activators of Lecithin-Cholesterol Acyltransferase(Nature Portfolio, 2024) Niemela, Akseli; Giorgi, Laura; Nouri, Sirine; Yurttas, Betul; Rauniyar, Khushbu; Jeltsch, Michael; Koivuniemi, ArtturiLecithin-cholesterol acyltransferase (LCAT) serves as a pivotal enzyme in preserving cholesterol homeostasis via reverse cholesterol transport, a process closely associated with the onset of atherosclerosis. Impaired LCAT function can lead to severe LCAT deficiency disorders for which no pharmacological treatment exists. LCAT-based therapies, such as small molecule positive allosteric modulators (PAMs), against LCAT deficiencies and atherosclerosis hold promise, although their efficacy against atherosclerosis remains challenging. Herein we utilized a quantitative in silico metric to predict the activity of novel PAMs and tested their potencies with in vitro enzymatic assays. As predicted, sodium-glucose cotransporter 2 (SGLT2) inhibitors (gliflozins), sucrose and flavonoids activate LCAT. This has intriguing implications for the mechanism of action of gliflozins, which are commonly used in the treatment of type 2 diabetes, and for the endogenous activation of LCAT. Our results underscore the potential of molecular dynamics simulations in rational drug design.Article Citation - WoS: 19Citation - Scopus: 20Experimental Investigation of Zinc Ferrite/Insulation Oil Nanofluid Natural Convection Heat Transfer, Ac Dielectric Breakdown Voltage, and Thermophysical Properties(Nature Portfolio, 2024) Pourpasha, Hadi; Heris, Saeed Zeinali; Javadpour, Reza; Mohammadpourfard, Mousa; Li, YaqingImproving the thermal and dielectric properties of insulation oil (INO) with nanoadditives is an important challenge, and achieving dispersion stability in these nanofluids is quite challenging, necessitating further investigation. The main goal of this study is the synthesis and use of the hydrophobicity of zinc ferrite (ZnFe2O4) nanoparticles, which can improve both the thermal and dielectric properties of the INO. This oil is made from distillate (petroleum), including severely hydrotreated light naphthenic oil (75-85%) and severely hydrotreated light paraffinic oil (15-25%). A comprehensive investigation was carried out, involving the creation of nanofluids with ZnFe2O4 nanoparticles at various concentrations, and employing various characterization methods such as X-ray diffraction (XRD), Fourier-transform infrared (FTIR), scanning electron microscopy, energy dispersive X-ray (EDX), zeta potential analysis, and dynamic light scattering (DLS). The KD2 Pro thermal analyzer was used to investigate the thermal characteristics, including the thermal conductivity coefficient (TCC) and volumetric heat capacity (VHC). Under free convection conditions, the free convection heat transfer coefficient (FCHTC) and Nusselt numbers (Nu) were evaluated, revealing enhancements ranging from 14.15 to 11.7%. Furthermore, the most significant improvement observed in the AC Breakdown voltage (BDV) for nanofluids containing 0.1 wt% of ZnFe2O4 amounted to 17.3%. The most significant finding of this study is the improvement in the heat transfer performance, AC BDV, and stability of the nanofluids.Article Citation - WoS: 13Citation - Scopus: 13The Influence of Nano Filter Elements on Pressure Drop and Pollutant Elimination Efficiency in Town Border Stations(Nature Portfolio, 2023) Ebadiyan, Hamed; Heris, Saeed Zeinali; Mousavi, Seyed Borhan; Nami, Shamin Hosseini; Mohammadpourfard, MousaNatural gas stands as the most ecologically sustainable fossil fuel, constituting nearly 25% of worldwide primary energy utilization and experiencing rapid expansion. This article offers an extensive comparative analysis of nano filter elements, focusing on pressure drop and pollutant removal efficiency. The primary goal was to assess the superior performance of nano filter elements and their suitability as an alternative for Town Border Station (TBS). The research encompassed a six-month examination period, involving routine pressure assessments, structural examinations, and particle characterization of the filter elements. The results revealed that nano filters showed better performance in adsorbing aluminum than conventional filters, possibly due to their cartridge composition. Nano filters contained phosphorus, sulfur, and copper, while conventional filters lacked these elements. The disparity can be attributed to the finer mesh of the nano filter, capturing smaller pollutants. Although the nano filter had minimal silicon, the conventional filter showed some, posing concerns. Despite having 19 extra pleats, the nano filter maintained gas flow pressure while capturing more particles than the conventional filter.Article Citation - WoS: 22Citation - Scopus: 23A Single-Amino Acid Substitution in the Adaptor Lat Accelerates Tcr Proofreading Kinetics and Alters T-Cell Selection, Maintenance and Function(Nature Portfolio, 2023) Lo, Wan-Lin; Ekiz, Hüseyin Atakan; Kuhlmann, Miriam; Rizzuto, Gabrielle; Ekiz, H. Atakan; Kolawole, Elizabeth M.; Revelo, Monica P.; Andargachew, RakiebMature T cells must discriminate between brief interactions with self-peptides and prolonged binding to agonists. The kinetic proofreading model posits that certain T-cell antigen receptor signaling nodes serve as molecular timers to facilitate such discrimination. However, the physiological significance of this regulatory mechanism and the pathological consequences of disrupting it are unknown. Here we report that accelerating the normally slow phosphorylation of the linker for activation of T cells (LAT) residue Y136 by introducing an adjacent Gly135Asp alteration (LAT(G135D)) disrupts ligand discrimination in vivo. The enhanced self-reactivity of LAT(G135D) T cells triggers excessive thymic negative selection and promotes T-cell anergy. During Listeria infection, LAT(G135D) T cells expand more than wild-type counterparts in response to very weak stimuli but display an imbalance between effector and memory responses. Moreover, despite their enhanced engagement of central and peripheral tolerance mechanisms, mice bearing LAT(G135D) show features associated with autoimmunity and immunopathology. Our data reveal the importance of kinetic proofreading in balancing tolerance and immunity. Lo and colleagues provide evidence for the TCR kinetic proofreading model by LAT Gly135Asp alteration to reveal functional consequences of altered kinetics in TCR activation in thymic selection and mature T-cell responses.