PubMed İndeksli Yayınlar Koleksiyonu / PubMed Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/11147/7645
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Article Phenotypically Plastic Drug-Resistant Chronic Myeloid Leukaemia Cell Line Displays Enhanced Cellular Dynamics in a Zebrafish Xenograft Model(Wiley, 2024) Özhan, Güneş; Yuce, Zeynep; Ozhan, Gunes; 04.03. Department of Molecular Biology and Genetics; 04. Faculty of Science; 01. Izmir Institute of TechnologyUnderstanding 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) Arslan Yıldız, Ahu; Karabacak, Soner; Yıldız, Ümit Hakan; Yildiz, Umit Hakan; 04.01. Department of Chemistry; 03.01. Department of Bioengineering; 03. Faculty of Engineering; 04. Faculty of Science; 01. Izmir Institute of TechnologyThis 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) Akgül, Bünyamin; Yurtsever, Yigit; Akgul, Bunyamin; 04.03. Department of Molecular Biology and Genetics; 04. Faculty of Science; 01. Izmir Institute of TechnologyEndoplasmic 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) Elçi, Şebnem; Elci, Sebnem; 03.03. Department of Civil Engineering; 03. Faculty of Engineering; 01. Izmir Institute of TechnologyThermal 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) Akgül, Bünyamin; Erdoğan, İpek; Vatansever, Ipek Erdogan; Akgul, Buenyamin; 04.03. Department of Molecular Biology and Genetics; 04. Faculty of Science; 01. Izmir Institute of TechnologyCell 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.