Erdoğan, İpek
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Erdogan, Ipek
Erdoğan Vatansever, İpek
Erdoğan, Ipek
Erdoğan, İ.
Erdoğan, İ
Erdogan, I.
Erdogan, I
Erdoğan Vatansever, İpek
Erdoğan, Ipek
Erdoğan, İ.
Erdoğan, İ
Erdogan, I.
Erdogan, I
Job Title
Email Address
ipekerdogan@iyte.edu.tr
Main Affiliation
04.03. Department of Molecular Biology and Genetics
Status
Current Staff
Website
ORCID ID
Scopus Author ID
Turkish CoHE Profile ID
Google Scholar ID
WoS Researcher ID
Sustainable Development Goals
1NO POVERTY
0
Research Products
2ZERO HUNGER
2
Research Products
3GOOD HEALTH AND WELL-BEING
10
Research Products
4QUALITY EDUCATION
0
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5GENDER EQUALITY
0
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6CLEAN WATER AND SANITATION
1
Research Products
7AFFORDABLE AND CLEAN ENERGY
2
Research Products
8DECENT WORK AND ECONOMIC GROWTH
0
Research Products
9INDUSTRY, INNOVATION AND INFRASTRUCTURE
3
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10REDUCED INEQUALITIES
0
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11SUSTAINABLE CITIES AND COMMUNITIES
0
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12RESPONSIBLE CONSUMPTION AND PRODUCTION
2
Research Products
13CLIMATE ACTION
2
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14LIFE BELOW WATER
0
Research Products
15LIFE ON LAND
0
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16PEACE, JUSTICE AND STRONG INSTITUTIONS
0
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17PARTNERSHIPS FOR THE GOALS
0
Research Products
Documents
13
Citations
222
h-index
8
Documents
22
Citations
218
Scholarly Output
23
Articles
14
Views / Downloads
98914/8571
Supervised MSc Theses
1
Supervised PhD Theses
1
WoS Citation Count
214
Scopus Citation Count
240
Patents
0
Projects
0
WoS Citations per Publication
9.30
Scopus Citations per Publication
10.43
Open Access Source
22
Supervised Theses
2
| Journal | Count |
|---|---|
| Turkish Journal of Biology | 3 |
| European Journal of Pharmaceutical Sciences | 2 |
| Romanian Biotechnological Letters | 2 |
| Frontiers in Genetics | 2 |
| Frontiers in Cell and Developmental Biology | 1 |
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Scopus Quartile Distribution
Competency Cloud
23 results
Scholarly Output Search Results
Now showing 1 - 10 of 23
Dataset Knockdown of death receptor 5 antisense long noncoding RNA and cisplatin treatment modulate similar macromolecular and metabolic changes in HeLa cells(TÜBİTAK, 2022-12) Gürer, Dilek Cansu; Erdoğan Vatansever, İpek; Ceylan, Çağatay; Akgül, BünyaminBackground/aim: Despite great progress in complex gene regulatory mechanisms in the dynamic tumor microenvironment, the potential contribution of long noncoding RNAs (lncRNAs) to cancer cell metabolism is poorly understood. Death receptor 5 antisense (DR5-AS) is a cisplatin inducible lncRNA whose knockdown modulates cell morphology. However, its effect on cell metabolism is unknown. The aim of this study is to examine metabolic changes modulated by cisplatin and DR5-AS lncRNA in HeLa cells. Materials and methods: We used cisplatin as a universal cancer therapeutic drug to modulate metabolic changes in HeLa cervix cancer cells. We then examined the extent of metabolic changes by Fourier transform infrared spectroscopy (FTIR). We also performed transcriptomics analyses by generating new RNA-seq data with total RNAs isolated from cisplatin-treated HeLa cells. Then, we compared cisplatin-mediated transcriptomics and macromolecular changes with those mediated by DR5-AS knockdown. Results: Cisplatin treatment caused changes in the unsaturated fatty acid and lipid-to-protein ratios and the glycogen content. These observations in altered cellular metabolism were supported by transcriptomics analyses. FTIR spectroscopy analyses have revealed that DR5-AS knockdown causes a 20.9% elevation in the lipid/protein ratio and a 76.6% decrease in lipid peroxidation. Furthermore, we detected a 3.42% increase in the chain length of the aliphatic lipids, a higher content of RNA, and a lower amount of glycogen indicating relatively lower metabolic activity in the DR5-AS knockdown HeLa cells. Interestingly, we observed a similar gene expression pattern under cisplatin treatment and DR5-AS knockdown HeLa cells. Conclusion: These results suggest that DR5-AS lncRNA appears to account for a fraction of cisplatin-mediated macromolecular and metabolic changes in HeLa cervix cancer cells. Turkish Journal of Biology dergisine gönderilmiş "Knockdown of death receptor 5 antisense long noncoding RNA and cisplatin treatment modulate similar macromolecular and metabolic changes in HeLa cells" isimli makalenin supplementary data dosyalarını içerir. 117Z243 no'lu TÜBİTAK projesinin yürütücüsü Prof. Dr. Bünyamin AKGÜL'dür.Review Citation - WoS: 4Citation - Scopus: 4Unraveling the Intriguing Interplay: Exploring the Role of Lncrnas in Caspase-Independent Cell Death(Wiley, 2024) Ciftci, Yusuf Cem; Akgül, Bünyamin; Vatansever, Ipek Erdogan; Akgul, BuenyaminCell 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.Article Citation - WoS: 14Citation - Scopus: 15Noncoding Rnas in Apoptosis: Identification and Function(TÜBİTAK, 2022) Tüncel, Özge; Kara, Merve; Yaylak, Bilge; Erdoğan, İpek; Akgül, BünyaminApoptosis is a vital cellular process that is critical for the maintenance of homeostasis in health and disease. The derailment of apoptotic mechanisms has severe consequences such as abnormal development, cancer, and neurodegenerative diseases. Thus, there exist complex regulatory mechanisms in eukaryotes to preserve the balance between cell growth and cell death. Initially, protein coding genes were prioritized in the search for such regulatory macromolecules involved in the regulation of apoptosis. However, recent genome annotations and transcriptomics studies have uncovered a plethora of regulatory noncoding RNAs that have the ability to modulate not only apoptosis but also many other biochemical processes in eukaryotes. In this review article, we will cover a brief summary of apoptosis and detection methods followed by an extensive discussion on microRNAs, circular RNAs, and long noncoding RNAs in apoptosis.Doctoral Thesis Preparation and Characterization of Wound Dressing Contact Layer(Izmir Institute of Technology, 2015) Erdoğan, İpek; Bayraktar, Oğuz; Atabey, Atay; Başal Bayraktar, GüldemetWound dressings provide therapeutic and protective features and promotes natural healing process when applied to a wound area. Being non-toxic and immunologically inert, natural biopolymers have potential in fabrication of wound dressings. Growth factors and antibiotics can also be used in functionalization of wound dressings as well as plant extracts. Olive leaf extract has gained attraction due to its dual antimicrobial and antioxidant effect. By clearing pathogenic microorganisms and scavenging against increased amount of reactive oxygen species in the wound area, it has high potential in wound healing. In this study, olive leaf extract incorporated zein fibers were prepared as a model of wound dressing contact layer. In this regard, crude olive leaf extract was fractionated and characterized in terms of antioxidant capacity, total phenol content and antimicrobial activity. Crude extract and its fractions were also subjected to wound scratch assay in the presence of hydrogen peroxide. Oleuropein, as the most abundant component in crude extract, was found to promote cell migration better and close the wound area at a higher rate than other components. On the other hand, crude olive leaf extract exhibited higher percentage of wound closure than its fractions within the same time period, which may be attributed to synergistic effect of unidentified phenolics. Crude olive leaf extract also provided crosslinking effect when incorporated into zein fibers, as well as promoting cell spreading behaviour.Book Part Citation - WoS: 30Citation - Scopus: 41Nanocarriers for Plant-Derived Natural Compounds(Elsevier Ltd., 2017) Bayraktar, Oğuz; Erdoğan, İpek; Köse, Merve D.; Kalmaz, GülcanNatural products constitute a large fraction in drug discovery processes. The term includes compounds from plants, microorganisms, and animals. Most of the natural products are secondary metabolites derived from plants, which are low in amounts and difficult to isolate. Another issue is the preservation of their bioactivity during process and storage as well as degradation in the gastrointestinal system before reaching circulation. Advances in nanotechnology offer nanoparticles, nanocapsules, and conjugates, which are devoted to site-specific, time-controlled delivery of bioactive agents. Nanoencapsulated systems have the advantage of high drug encapsulation efficiency because of optimized drug solubility in the core, low polymer content compared to other nanoparticulated systems such as nanospheres, drug polymeric shell protection against degradation factors, and the reduction of tissue irritation caused by the polymeric shell. This chapter will discuss nanoencapsulation methods and advances in carrier systems for plant-derived natural compounds.Article Citation - WoS: 6Citation - Scopus: 8Deep Sequencing Reveals Two Jurkat Subpopulations With Distinct Mirna Profiles During Camptothecin-Induced Apoptosis(TUBITAK, 2018) Erdoğan, İpek; Coşacak, Mehmet İlyas; Nalbant, Ayten; Akgül, BünyaminMicroRNAs (miRNAs) are small noncoding RNAs of about 19-25 nt that regulate gene expression posttranscriptionally under various cellular conditions, including apoptosis. The miRNAs involved in modulation of apoptotic events in T cells are partially known. However, heterogeneity associated with cell lines makes it difficult to interpret gene expression signatures, especially in cancer-related cell lines. Treatment of the Jurkat T-cell leukemia cell line with the universal apoptotic drug, camptothecin, resulted in identification of two Jurkat subpopulations: one that is sensitive to camptothecin and another that is rather intrinsically resistant. We sorted apoptotic Jurkat cells from nonapoptotic ones prior to profiling miRNAs through deep sequencing. Our data showed that a total of 184 miRNAs were dysregulated. Interestingly, the apoptotic and nonapoptotic subpopulations exhibited distinct miRNA expression profiles. In particular, 6 miRNAs were inversely expressed in these two subpopulations. The pyrosequencing results were validated by real-time qPCR. Altogether, these results suggest that miRNAs modulate apoptotic events in T cells and that cellular heterogeneity requires careful interpretation of miRNA expression profiles obtained from drug-treated cell lines.Article Citation - WoS: 19Citation - Scopus: 24Intracytoplasmic Re-Localization of Mirisc Complexes(Frontiers Media S.A., 2018) Akgül, Bünyamin; Erdoğan, İpekMicroRNAs (miRNAs) are a conserved class of non-coding RNAs of 22 nucleotides that post-transcriptionally regulate gene expression through translational repression and/or mRNA degradation. A great progress has been made regarding miRNA biogenesis and miRNA-mediated gene regulation. Additionally, an ample amount of information exists with respect to the regulation of miRNAs. However, the cytoplasmic localization of miRNAs and its effect on gene regulatory output is still in progress. We provide a current review of the cytoplasmic miRNA localization in metazoans. We then discuss the dynamic changes in the intracytoplasmic localization of miRNAs as a means to regulate their silencing activity. We then conclude our discussion with the potential molecules that could modulate miRNA localization.Master Thesis Identification of Micrornas Involved in Camptothecin-Induced Apoptosis in Jurkat T Cell Line(Izmir Institute of Technology, 2008) Erdoğan, İpek; Akgül, BünyaminMicroRNAs which are non-coding RNAs 19-25 nt in length regulate gene expression at post-transcriptional and translational stages. Although it is known that they play a role in critical processes such as development and differentiation of T cells a major component of the immune system, the function of miRNAs in T cell apoptosis is unknown. This study has aimed to identify miRNAs. involvement in camptothecininduced T cell apoptosis in the Jurkat T cell leukemia cell line model. Following the enrichment of the apoptotic population by magnetic seperation, the negative and apoptotic fractions were profilled and compared according to the expression levels of microRNAs. Out of the 866 miRNAs in the miRBASE, 37 and 58 of them were downand up-regulated in the apoptotic fraction, respectively. 7 miRNAs were members of the clusters that have predicted targets as anti-apoptotic genes and tumour suppressor proteins. 66 miRNAs have no known function. Candidate miRNAs, selected based on their higher differential expression levels with predicted apoptotic/antiapoptotic targets, will be verified by qPCR. These candidate then will be further characterized by overxpression and knock-down studies.Article Citation - WoS: 11Citation - Scopus: 10Genomewide M6a Mapping Uncovers Dynamic Changes in the M6a Epitranscriptome of Cisplatin-Treated Apoptotic Hela Cells(MDPI, 2022) Akçaöz, Azime; Tüncel, Özge; Gelmez, Ayşe Bengisu; Sağlam, Buket; Erdoğan Vatansever, İpek; Akgül, BünyaminCisplatin (CP), which is a conventional cancer chemotherapeutic drug, induces apoptosis by modulating a diverse array of gene regulatory mechanisms. However, cisplatin-mediated changes in the m6A methylome are unknown. We employed an m6A miCLIP-seq approach to investigate the effect of m6A methylation marks under cisplatin-mediated apoptotic conditions on HeLa cells. Our high-resolution approach revealed numerous m6A marks on 972 target mRNAs with an enrichment on 132 apoptotic mRNAs. We tracked the fate of differentially methylated candidate mRNAs under METTL3 knockdown and cisplatin treatment conditions. Polysome profile analyses revealed perturbations in the translational efficiency of PMAIP1 and PHLDA1 transcripts. Congruently, PMAIP1 amounts were dependent on METTL3. Additionally, cisplatin-mediated apoptosis was sensitized by METTL3 knockdown. These results suggest that apoptotic pathways are modulated by m6A methylation events and that the METTL3–PMAIP1 axis modulates cisplatin-mediated apoptosis in HeLa cells.Article Citation - WoS: 30Citation - Scopus: 35Bioactive Sheath/Core Nanofibers Containing Olive Leaf Extract(John Wiley and Sons Inc., 2016) Doğan, Gamze; Başal, Güldemet; Bayraktar, Oğuz; Özyıldız, Figen; Uzel, Ataç; Erdoğan, İpekThis study aimed at producing silk fibroin (SF)/hyaluronic acid (HA) and olive leaf extract (OLE) nanofibers with sheath/core morphology by coaxial electrospinning method, determining their antimicrobial properties, and examining release profiles of OLE from these coaxial nanofibers. Optimum electrospinning process and solution parameters were determined to obtain uniform and bead-free coaxial nanofibers. Scanning electron microscopy and transmission electron microscopy (TEM) were used to characterize the morphology of the nanofibers. The antimicrobial activities of nanofibers were tested according to AATCC test method 100. Total phenolic content and total antioxidant activity were tested using in vitro batch release system. The quality and quantity of released components of OLE were determined by high-performance liquid chromatography. The changes in nanofibers were examined by Fourier-transform infrared spectroscopy. Uniform and bead-free nanofibers were produced successfully. TEM images confirmed the coaxial structure. OLE-loaded nanofibers demonstrated almost perfect antibacterial activities against both of gram-negative and gram-positive bacteria. Antifungal activity against C. albicans was rather poor. After a release period of 1 month, it was observed that ∼70-95% of the OLE was released from nanofibers and it was still bioactive. Overall results indicate that the resultant shell/core nanofibers have a great potential to be used as biomaterials.
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