Özkaya, Ali Burak
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Ozkaya, Ali Burak
Ozkaya, A. B.
Ozkaya, A. Burak
Ozkaya, Ali B.
Ozkaya, A. B.
Ozkaya, A. Burak
Ozkaya, Ali B.
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Email Address
ali.ozkaya@ieu.edu.tr
Main Affiliation
09.01. Basic Medical Sciences
Status
Current Staff
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Sustainable Development Goals
11
SUSTAINABLE CITIES AND COMMUNITIES
0
Research Products
4
QUALITY EDUCATION
0
Research Products
8
DECENT WORK AND ECONOMIC GROWTH
0
Research Products
12
RESPONSIBLE CONSUMPTION AND PRODUCTION
0
Research Products
9
INDUSTRY, INNOVATION AND INFRASTRUCTURE
1
Research Products
15
LIFE ON LAND
0
Research Products
6
CLEAN WATER AND SANITATION
0
Research Products
1
NO POVERTY
0
Research Products
7
AFFORDABLE AND CLEAN ENERGY
0
Research Products
10
REDUCED INEQUALITIES
0
Research Products
14
LIFE BELOW WATER
0
Research Products
2
ZERO HUNGER
0
Research Products
13
CLIMATE ACTION
0
Research Products
5
GENDER EQUALITY
0
Research Products
16
PEACE, JUSTICE AND STRONG INSTITUTIONS
0
Research Products
17
PARTNERSHIPS FOR THE GOALS
0
Research Products
3
GOOD HEALTH AND WELL-BEING
3
Research Products
Documents
16
Citations
238
h-index
10
Documents
22
Citations
201
Scholarly Output
9
Articles
8
Views / Downloads
20/58
Supervised MSc Theses
0
Supervised PhD Theses
0
WoS Citation Count
54
Scopus Citation Count
80
WoS h-index
4
Scopus h-index
4
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0
Projects
1
WoS Citations per Publication
6.00
Scopus Citations per Publication
8.89
Open Access Source
6
Supervised Theses
0
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| Journal | Count |
|---|---|
| Turkısh Journal of Bıochemıstry-Turk Bıyokımya Dergısı | 2 |
| Drug Development And Industrıal Pharmacy | 1 |
| FEBS Open Bio | 1 |
| Acıbadem Üniversitesi Sağlık Bilimleri Dergisi | 1 |
| Plos One | 1 |
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9 results
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Now showing 1 - 9 of 9
Article ?-Hydroxybutyrate Does Not Influence Viability and Clonogenicity of A549 Lung Cancer Cells(2023) Özkaya, Ali Burak; Malcanlı, Semanur; Geyik, Öykü GönülBackground/Purpose: The metabolic shift from catabolism of carbohydrates to lipids results in production of ketone bodies leading to a state called ketosis. Ketosis via ketone supplement or ketogenic diet has been proposed as a non-toxic therapeutic option for a broad range of malignancies. Although the clinical impact of ketogenic diet is well-documented, the effect of ketone bodies on cancer cell biology is not clear for some cancers including non-small-cell lung cancer (NSCLC). In this study, we aimed to demonstrate the effects of the most prominent ketone body, ?-hydroxybutyrate, on a NSCLC cell line, A549. Methods: A549 cell line was utilized as the in vitro model in this study. The effects of different ?-hydroxybutyrate concentrations on cell viability were measured via sulphorodamine-B (SRB) viability assay. Long term effects of ketosis were evaluated via colony formation assay. Finally, the effect of ?-hydroxybutyrate on cell migration was determined via scratch assay. Results: Our results suggest that introduction of ?-hydroxybutyrate in physiologically relevant concentrations into the cell culture media does not influence cell viability, clonogenicity or migration. Conclusion: ?-hydroxybutyrate has been previously demonstrated to induce, inhibit or does not influence the viability of different cell lines but there is no report regarding its effects on NSCLC cells. Here we report that physiologically relevant concentrations of ?-hydroxybutyrate have no effect on viability, clonogenicity and migration of A549 cells.Article Most Autophagic Cell Death Studies Lack Evidence of Causality(Wiley, 2025) Ozkaya, Ali Burak; Ghaseminejad, YasminAutophagy plays a critical role in maintaining cellular homeostasis and is implicated in various physiological and pathological processes, including cancer, neurodegeneration, and metabolic disorders. Although typically associated with cell survival, autophagy has also been proposed to contribute to cell death, referred to as autophagic cell death (ACD). However, the identification of ACD remains contentious due to inconsistencies in experimental methodologies and terminological misuse.In this study, we systematically evaluated 104 research articles published in 2022 that claimed to demonstrate ACD. Articles were assessed based on established criteria, including evidence for autophagy, evidence for cell death, exclusion of apoptosis, and experimental designs demonstrating causality. Our findings reveal that only 12.5% of the articles fulfilled all ACD criteria, while 37.5% provided only correlation-level evidence. Additionally, 54.81% failed to demonstrate autophagy flux, 32.7% relied on viability loss rather than direct evidence of cell death, and 45.0% of studies utilizing autophagy inhibition failed to demonstrate actual inhibition of autophagy. Inconsistent terminology was also prevalent, with "autophagy-mediated cell death" often misclassified as ACD and ACD frequently misused to describe autophagy co-occurring with cell death.These issues highlight a lack of rigor in current practices, with correlation-level evidence, inappropriate experimental designs, and terminological misuse undermining study robustness. To address these challenges, we developed a systematic workflow providing experimental and analytical guidance for classifying evidence for different modes of autophagy. Our analysis underscores the need for greater rigor, standardized approaches, and precise terminology to advance understanding of the interplay between autophagy and cell death.Review Citation - WoS: 16Citation - Scopus: 40Current Evaluation and Recommendations for the Use of Artificial Intelligence Tools in Education(Walter De Gruyter Gmbh, 2023) Sagin, Ferhan Girgin; Özkaya, Ali Burak; Tengiz, Funda; Geyik, Öykü Gönül; Geyik, CanerThis paper discusses the integration of artificial intelligence (AI) tools in education, delineating their potential to transform pedagogical practices alongside the challenges they present. Generative AI models like ChatGPT, had a disruptive impact on teaching and learning, due to their ability to create text, images, and sound, revolutionizing educational content creation and modification. However, nowadays the educational community is polarized, with some embracing AI for its accessibility and efficiency thus advocating it as an indispensable tool, while others cautioning against risks to academic integrity and intellectual development. This document is designed to raise awareness about AI tools and provide some examples of how they can be used to improve education and learning. From an educator's perspective, AI is an asset for curriculum development, course material preparation, instructional design and student assessment, while reducing bias and workload. For students, AI tools offer personalized learning experiences, timely feedback, and support in various academic activities. The Turkish Biochemical Society (TBS) Academy recommends educators to embrace and utilize AI tools to enhance educational processes, and engage in peer learning for better adaptation while maintaining a critical perspective on their utility and limitations. The transfer of AI knowledge and methods to the teaching experiences should complement and not replace the educator's creativity and critical thinking. The paper advocates for an informed embrace of AI, AI fluency among educators and students, ethical application of AI in academic settings, and continuous engagement with the evolving AI technologies, ensuring that AI tools are used to augment critical thinking and contribute positively to education and society.Article Citation - WoS: 6Citation - Scopus: 5Acrylamide-Encapsulated Glucose Oxidase Inhibits Breast Cancer Cell Viability(Walter De Gruyter Gmbh, 2020) Rrustemi, Trendelina; Geyik, Oyku Gonul; Ozkaya, Ali Burak; Ozturk, Taylan Kurtulus; Yuce, Zeynep; Kilinc, AliObjectives: Cancer cells modulate metabolic pathways to ensure continuity of energy, macromolecules and redoxhomeostasis. Although these vulnerabilities are often targeted individually, targeting all with an enzyme may prove a novel approach. However, therapeutic enzymes are prone to proteolytic degradation and neutralizing antibodies leading to a reduced half-life and effectiveness. We hypothesized that glucose oxidase (GOX) enzyme that catalyzes oxidation of glucose and production of hydrogen peroxide, may hit all these targets by depleting glucose; crippling anabolic pathways and producing reactive oxygen species (ROS); unbalancing redox homeostasis. Methods: We encapsulated GOX in an acrylamide layer and then performed activity assays in denaturizing settings to determine protection provided by encapsulation. Afterwards, we tested the effects of encapsulated (enGOX) and free (fGOX) enzyme on MCF-7 breast cancer cells. Results: GOX preserved 70% of its activity following encapsulation. When fGOX and enGOX treated with guanidinium chloride, fGOX lost approximately 72% of its activity, while enGOX only lost 30%. Both forms demonstrated remarkable resilience against degradation by proteinase K and inhibited viability of MCF-7 cells in an activity-dependent manner. Conclusions: Encapsulation provided protection to GOX against denaturation without reducing its activity, which would prolong half-life of the enzyme when administered intravenously.Article Citation - WoS: 23Citation - Scopus: 26Y Design and Development of a Self-Microemulsifying Drug Delivery System of Olmesartan Medoxomil for Enhanced Bioavailability(Taylor & Francis Ltd, 2019) Komesli, Yelda; Ozkaya, Ali Burak; Ergur, Bekir Ugur; Kirilmaz, Levent; Karasulu, ErcumentOlmesartan medoxomil (OM) is a hydrophobic antihypertensive drug with low bioavailability (26%) and is known to have adverse effects such as celiac disease and enteropathy. The purpose of this study was to develop SMEDDS to increase bioavailability and decrease potential side effects of OM. Hydrophilic lipophilic balance was calculated by testing solubility of OM in different oils, surfactants, and cosurfactants to obtain the most suitable combination of SMEDDS. Pseudoternary phase diagram was used to select the better oil/water formulation of SMEDDS. After a test for 3-month stability, dissolution tests and parallel artificial membrane permeability assay (PAMPA) were conducted to investigate drug solubility and permeability. Biodistribution of fluorescent marked SMEDDS was observed by using in vivo imaging system. The pharmacodynamics of the drug were determined by measuring blood pressure from tails of rats. At the end of the experiment, intestines were examined for adverse effects of OM. Compared with tablet formulation according to the dissolution study, SMEDDS formulation showed 1.67 times improvement in solubility of OM. PAMPA studies suggested a much faster permeability rate for OM SMEDDS compared to the suspension form. Labeled SMEDDS gave 3.96 times stronger fluorescent emission than control dye administered mice in in vivo imaging system (IVISA (R)) studies, indicating an increased bioavailability. Treating effect of SMEDDS was 3.1 times more efficient compared to suspension in hypertensive rats. It caused neither celiac-like enteropathy nor diarrhea, during 21-day noninvasive blood pressure system (NIBP) assay. Our results suggest that SMEEDS formulation improves dissolution and oral bioavailability of OM while reducing its adverse effects.Article Prolonged Β-Hydroxybutyrate Ketosis Enhances Ponatinib Response of K562 Chronic Myeloid Leukaemia Cells(Dokuz Eylul Univ inst Health Sciences, 2025) Özkaya, Ali Burak; Geyik, Öykü Gönül; Malcanlı, SenanurPurpose: Ketosis is a metabolic state characterized by production of ketone bodies, including acetoacetate, β-hydroxybutyrate (BHB), and acetone, in response to reduced blood glucose levels. BHB stands out as the principal ketone body in nutritional ketosis which has diverse therapeutic implications for metabolic, nondegenerative and neoplastic disorders. In current study we investigated the impact of ketosis on chronic myeloid leukaemia (CML) cell viability and drug response. Materials and Methods: We investigated the impact of BHB-mediated ketosis on the viability of K562 cells, an in vitro model of CML, and explored the influence of BHB on the sensitivity of these cells to ponatinib, a multi-targeted tyrosine kinase inhibitor used in CML treatment. We used MTT assay to measure cell viability and Hoechst/PI assay to measure cell death. Results: Our findings reveal that BHB concentrations ranging from 1 mM to 5 mM, which fall within the physiological range of ketosis, elicit a minimal yet concentration-dependent reduction in cell viability. We also observed that while a 24-hour pre-treatment with BHB did not enhance the response of K562 cells to ponatinib, prolonged ketosis (4 days) improved response of cells to the drug by decreasing final cell viability from 25.15% to 13.12%. The primary mode of viability inhibition by ponatinib was cell death which was further intensified by exposure to prolonged ketosis. Conclusion: Ketosis induced by ketogenic diet of ketone body supplementation is considered as safe and effective adjuvant cancer therapy options and here, we report its potential effectiveness in the context of CML.Article Multidisciplinary Case-Based Small Group Discussions To Integrate Basic Medical Sciences With Clinical Situations(Walter De Gruyter Gmbh, 2022) Şemin, Makbule İlgi; Ersil Soysal, Dilek; Seval Çelik, Yasemin; Hayran, Murvet; Demir, Ayse Banu; Ozkaya, Ali Burak; İnan, Sevinç; Akdoğan, GülObjectives Integration of the basic medical sciences with clinical medicine motivates medical students by showing how the fundamental concepts they have learned will come into their future practice. In this context, we created clinical integration sessions (CIS) in our first-year medical curriculum. Methods The instructors of different disciplines wrote the clinical scenarios together. The scenarios were discussed in five sessions with 39 first-year students. The first session's scenario consisted of four brief anemia cases. The next four sessions included a single case, according to the feedback of the students. Students formed groups of 7-8 participants. In the first 2 h, the scenarios were discussed in the groups and questions were answered by the students. In the third hour, the instructors answered the questions together with the students. After the first CIS, written feedback obtained from the students via a survey. Results The survey provided positive feedback on the benefits of active learning within small group discussions, and most of the students thought that their background was sufficient to solve the cases, with some literature search. Conclusion The scenarios, which provide multidisciplinary integration of basic medical sciences and clinical medicine, can be useful educational materials.Article Citation - WoS: 9Citation - Scopus: 9From Viability To Cell Death: Claims With Insufficient Evidence in High-Impact Cell Culture Studies(Public Library Science, 2022) Ozkaya, Ali Burak; Geyik, CanerBackground Reliability of preclinical research is of critical concern. Prior studies have demonstrated the low reproducibility of research results and recommend implementing higher standards to improve overall quality and robustness of research. One understudied aspect of this quality issue is the harmony between the research hypotheses and the experimental design in published work. Methods and findings In this study we focused on highly cited cell culture studies and investigated whether commonly asserted cell culture claims such as viability, cytotoxicity, proliferation rate, cell death and apoptosis are backed with sufficient experimental evidence or not. We created an open access database containing 280 claims asserted by 103 different high-impact articles as well as the results of this study. Our findings revealed that only 64% of all claims were sufficiently supported by evidence and there were concerning misinterpretations such as considering the results of tetrazolium salt reduction assays as indicators of cell death or apoptosis. Conclusions Our analysis revealed a discordance between experimental findings and the way they were presented and discussed in the manuscripts. To improve quality of pre-clinical research, we require clear nomenclature by which different cell culture claims are distinctively categorized; materials and methods sections to be written more meticulously; and cell culture methods to be selected and utilized more carefully. In this paper we recommend a nomenclature for selected cell culture claims as well as a methodology for collecting evidence to support those claims.Conference Object Bridging Science and Teaching: Active Learning Strategies for Molecular Life Scientists Learning Building(Wiley, 2025) Costa, Manuel Joao; Ozkaya, Ali Burak
