Scopus İndeksli Yayınlar Koleksiyonu / Scopus Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/11147/7148
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Article 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 A Quantitative Description of Barite Thermodynamics, Nucleation and Growth for Reactive Transport Modelling(Elsevier, 2024) Dideriksen,K.; Zhen-Wu,B.Y.; Dobberschütz,S.; Rodríguez-Blanco,J.D.; Raahauge,P.J.; Ataman, Evren; Stipp,S.L.S.The regression of available thermodynamic data in the BaSO4–NaCl–H2O system yielded Pitzer ion interaction parameters that accurately describe the activities of aqueous species and mineral solubilities in this system. This thermodynamics description is compared with published Pitzer parameter sets, and combined with a model for the kinetics of barite nucleation and growth, based on classical nucleation theory. Both the thermodynamic and nucleation/growth models have been incorporated into the PHREEQC computer code to facilitate calculation of the extent and consequences of barite formation in natural and engineered systems. Results of geochemical modelling calculations agree adequately with the amount of barite scale thicknesses derived from calliper measurements from an oil well if the effective surface free energy of barite nuclei is assumed to be ∼50 mJ m−2. Better results, however, are achieved using a temperature dependent effective surface free energy. In contrast, calculations performed by ignoring the effects of barite nucleation lead to a substantial overestimation of the amount of scale formed in our modelled systems. The success of our mineral nucleation and growth model to describe scaling in our modelled system suggests this description of precipitation rates can be applied to many other mineral-aqueous fluid systems, in particular where supersaturation is slight and the solids forming have substantial surface free energy. © 2024 Elsevier Ltd