Scopus İndeksli Yayınlar Koleksiyonu / Scopus Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/11147/7148
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Article A Comprehensive MicroRNA-Seq Transcriptomic Analysis of Tay-Sachs Disease Mice Revealed Distinct MiRNA Profiles in Neuroglial Cells(Springernature, 2025) Kaya, Beyza; Orhan, Mehmet Emin; Yanbul, Selman; Demirci, Muserref Duygu Sacar; Demir, Secil Akyildiz; Seyrantepe, VolkanTay-Sachs disease (TSD) is a rare lysosomal storage disorder marked by the progressive buildup of GM2 in the central nervous system (CNS). This condition arises from mutations in the HEXA gene, which encodes the alpha subunit of the enzyme beta-hexosaminidase A. A newly developed mouse model for early-onset TSD (Hexa-/-Neu3-/-) exhibited signs of neurodegeneration and neuroinflammation, evidenced by elevated levels of pro-inflammatory cytokines and chemokines, as well as significant astrogliosis and microgliosis. Identifying disease-specific microRNAs (miRNAs) may aid the development of targeted therapies. Although previous small-scale studies have investigated miRNA expression in some regions of GM2 gangliosidosis mouse models, thorough profiling of miRNAs in this innovative TSD model remains to be done. In this study, we employed next-generation sequencing to analyze the complete miRNA profile of neuroglial cells from Hexa-/-Neu3-/- mice. By comparing KEGG and Reactome pathways associated with neurodegeneration, neuroinflammation, and sphingolipid metabolism in Hexa-/-Neu3-/- neuroglial cells, we discovered new microRNAs and their targets related to the pathophysiology of GM2 gangliosidosis. For the first time, our findings showed that miR-708-5p, miR-672-5p, miR-204-5p, miR-335-5p, and miR-296-3p were upregulated, while miR-10 b-5p, miR-615-3p, miR-196a-5p, miR-214-5p, and miR-199a-5p were downregulated in Hexa-/-Neu3-/- neuroglial cells in comparison to age-matched wild-type (WT). These specific changes in miRNA expression deepen our understanding of the disease's neuropathological characteristics in Hexa-/-Neu3-/- mice. Our study suggests that miRNA-based therapeutic strategies may improve clinical outcomes for TSD patients.Article Citation - WoS: 1Citation - Scopus: 1The Role of Trna Fragments on Neurogenesis Alteration by H2o2-Induced Oxidative Stress(Springernature, 2025) Karacicek, Bilge; Katkat, Esra; Binokay, Leman; Ozhan, Gunes; Karakulah, Goekhan; Genc, SerminTransfer RNAs (tRNAs) are small non-coding RNA molecules transcribed from tRNA genes. tRNAs cleaved into a diverse population tRNA fragments (tRFs) ranging in length from 18 to 40 nucleotides, they interact with RNA binding proteins and influence the stability and translation. Stress is one of the reasons for tRFs cleavage. In our study, we modeled oxidative stress conditions with hydrogen peroxide (H2O2) exposure and dealt with one of the frequently expressed tRF in the hippocampus region of the brain, which is tRF-Glu-CTC. For this purpose, neural stem cells (NSCs) were exposed to H2O2, and tRF-Glu-CTC levels were increased in various H(2)O(2 )concentrations. A decrease was seen in microtubule-associated protein 2 (MAP2) marker expression. To understand the H(2)O(2)oxidative stress condition on the expression of tRNA fragments, 72 hpf zebrafish embryos exposed to different H(2)O(2 )concentrations, an increase in the level of tRF-Glu-CTC was observed in all concentrations of H(2)O(2 )compared to control. Subsequently, neurogenesis markers were figured out via Calb2a (calbindin 2a) in situ hybridization (ISH) and HuC/D immunofluorescence staining (IF) staining experiments. Under H(2)O(2 )exposure, a decline was observed in Calb2a and HuC/D markers. To understand the inhibitory role of tRF-Glu-CTC on neurogenesis, NSCs were transfected via tRF-Glu-CTC inhibitor, and neurogenesis markers (ss III-tubulin, MAP2, and GFAP) were determined with qRT-PCR and IF staining. tRF-Glu-CTC inhibitor reversed the diminished neuronal markers expression under the exposure of H2O2. Gene Ontology (GO) enrichment analysis showed us that targets of tRF-Glu-CTC are generally related to neuronal function and synaptic processes.Article Citation - WoS: 2Citation - Scopus: 2Origami-Inspired Microfluidic Paper-Based Analytical Device (μpad) for Microorganism Detection(Springernature, 2024) Sozmen, A. Baran; Bayraktar, A. Ezgi; Arslan-Yildiz, AhuPathogenic microorganisms impose great risk especially in resource-limited settings due to inaccessibility of diagnostic tools and monitoring devices. This is mainly caused by current methods often being economically demanding and complex in practice; while these methods are sensitive and accurate, they rarely follow Point-of-care (POC) approaches, which is essential for rapid detection and intervention. Incorporating origami into paper-based analytical devices (mu PAD) presents an innovative alternative, offering affordability, portability, and ease of disposal. Herein, a colorimetric origami mu PAD that is suitable for use in POC applications was developed. The mu PAD was fabricated via laser ablation utilizing PVDF and cellulose membranes. In order to develop the biosensor platform, fabrication parameters were optimized and hydrophilicity of PVDF membranes was improved using various solvents. The PVDF membranes were characterized through light microscopy imaging, protein adsorption assay and contact angle measurements. Then, optimization of the assay parameters was carried out in order to improve sensitivity and resolution of the mu PAD, utilizing Box-Behnken experimental design. The responses generated by the origami mu PAD in form of visible color development were then analyzed using image processing. After optimization is concluded, E. coli detection was carried out as a model system. Resulting calculations showed a limit of detection (LoD) of 2 CFU/mL and a dynamic working range up to 106 CFU/mL for E. coli. Overall, developed origami mu PAD promises an economic advantage compared to conventional methods, and provides rapid and sensitive results without the requirement of expertise or complex equipment.Review Citation - WoS: 7Citation - Scopus: 8Magnetic Levitation-Based Miniaturized Technologies for Advanced Diagnostics(Springernature, 2024) Karakuzu, Betul; Inevi, Muge Anil; Tarim, E. Alperay; Sarigil, Oyku; Guzelgulgen, Meltem; Kecili, Seren; Tekin, H. CumhurTaking advantage of the magnetic gradients created using magnetic attraction and repulsion in miniaturized systems, magnetic levitation (MagLev) technology offers a unique capability to levitate, orient and spatially manipulate objects, including biological samples. MagLev systems that depend on the inherent diamagnetic properties of biological samples provide a rapid and label-free operation that can levitate objects based on their density. Density-based cellular and protein analysis based on levitation profiles holds important potential for medical diagnostics, as growing evidence categorizes density as an important variable to distinguish between healthy and disease states. The parallel processing capabilities of MagLev-based diagnostic systems and their integration with automated tools accelerates the collection of biological data. They also offer notable advantages over current diagnostic techniques that require costly and labor-intensive protocols, which may not be accessible in a low-resource setting. MagLev-based diagnostic systems are user-friendly, portable, and affordable, making remote and label-free applications possible. This review describes the recent progress in the application of MagLev principles to existing problems in the field of diagnostics and how they help discover the molecular- and cellular-level changes that accompany the disease or condition of interest. The critical parameters associated with MagLev-based diagnostic systems such as magnetic medium, magnets, sample holders, and imaging systems are discussed. The challenges and barriers that currently limit the clinical implications of MagLev-based diagnostic systems are outlined together with the potential solutions and future directions including the development of compact microfluidic systems and hybrid systems by leveraging the power of deep learning and artificial intelligence.Article Citation - WoS: 1Citation - Scopus: 1Fractional Duals of the Poisson Process on Time Scales With Applications in Cryptography(Springernature, 2024) Gharari, Fatemeh; Hematpour, Nafiseh; Bakouch, Hassan S.; Popovic, Predrag M.A super-structure system for probability densities, covering not just typical types but also fractional ones, was developed using the time scale theory. From a mathematical point of view, we discover duals of the Poisson process on the time scale T=R\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\mathbb {T}=\mathbb {R}$$\end{document} for the time scales T=Z\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\mathbb {T}=\mathbb {Z}$$\end{document} and T=qZ,\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$ \mathbb {T}=q<^>{\mathbb {Z}},$$\end{document} evaluating del-\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\nabla -$$\end{document}calculus and Delta-\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\Delta -$$\end{document}calculus. Also, we search the fractional extensions of the Poisson process on these time scales and detect duals of them. A simulation allows for comparing the nabla and delta types of the observed distributions, not just typical types but also fractional ones. As an application, we also propose new substitution boxes (S-boxes) using the proposed stochastic models and compare the performance of S-boxes created in this way. Given that the S-box is the core for confusion in Advanced Encryption Standard (AES), the formation of these new S-boxes represents an interesting application of these stochastic models.Article Citation - WoS: 2Citation - Scopus: 4A Study on a Computationally Efficient Controller Design for a Surgical Robotic System(Springernature, 2023) Ayit, Orhan; Dede, Mehmet Ismet CanThe control algorithms of the surgical robotic system using the robot's dynamics produce a relatively high computational load on the processor. This paper develops a computationally efficient computed torque controller by using a simplified dynamic modeling method and implemented in a novel surgical robot experimentally. In addition, an independent joint controller is designed and implemented to compare the results of the computed torque controller.Article Citation - WoS: 1Citation - Scopus: 1Laser Surface Treatment Optimization of 1.2379 (Aisi D2) Tool Steel(Springernature, 2025) Ozbey, Sayit; Artem, Hatice SecilIndustrial applications require materials with specific surface quality and hardness properties. Laser surface treatment stands out as a cost-effective and effective method that improves surface performance by changing the structural and physical properties of the material. 1.2379 cold work tool steel is a commonly used material in die and mold industries for injection mold inserts; therefore, the surface properties of the material play a significant role. In this study, it is aimed to optimize laser parameters; the laser power, pulse duration, repetition rate and line spacing for the responses such as hardness and surface roughness. For this purpose, 1.2379 cold work tool surfaces were treated using a commercially available industrial ytterbium low-power pulsed fiber laser experimentally. Experiments were conducted based on 34 full factorials. Vickers hardness and micro-roughness measurements were performed on the laser-treated surfaces. Regression models were developed using experimental data and the appropriate models were selected for each response. The response variables were then optimized based on stochastic optimization methods: Nelder-Mead, Differential Evolution, Random Search and Simulated Annealing. The results indicate that a maximum hardness of 495 HV0.5 and a minimum surface roughness of 0.277 mu m were achieved, corresponding to a 61% increase and a 43% decrease, respectively, compared to the base metal.Article Citation - WoS: 37Citation - Scopus: 48Microfluidic-Based Virus Detection Methods for Respiratory Diseases(Springernature, 2021) Tarım, Ergün Alperay; Karakuzu, Betül; Öksüz, Cemre; Sarıgil, Öykü; Kızılkaya, Melike; Al-Ruweidi, Mahmoud Khatib A. A.; Yalçın, Hüseyin Çağatay; Özçivici, Engin; Tekin, Hüseyin CumhurWith the recent SARS-CoV-2 outbreak, the importance of rapid and direct detection of respiratory disease viruses has been well recognized. The detection of these viruses with novel technologies is vital in timely prevention and treatment strategies for epidemics and pandemics. Respiratory viruses can be detected from saliva, swab samples, nasal fluid, and blood, and collected samples can be analyzed by various techniques. Conventional methods for virus detection are based on techniques relying on cell culture, antigen-antibody interactions, and nucleic acids. However, these methods require trained personnel as well as expensive equipment. Microfluidic technologies, on the other hand, are one of the most accurate and specific methods to directly detect respiratory tract viruses. During viral infections, the production of detectable amounts of relevant antibodies takes a few days to weeks, hampering the aim of prevention. Alternatively, nucleic acid-based methods can directly detect the virus-specific RNA or DNA region, even before the immune response. There are numerous methods to detect respiratory viruses, but direct detection techniques have higher specificity and sensitivity than other techniques. This review aims to summarize the methods and technologies developed for microfluidic-based direct detection of viruses that cause respiratory infection using different detection techniques. Microfluidics enables the use of minimal sample volumes and thereby leading to a time, cost, and labor effective operation. Microfluidic-based detection technologies provide affordable, portable, rapid, and sensitive analysis of intact virus or virus genetic material, which is very important in pandemic and epidemic events to control outbreaks with an effective diagnosis.