Akgül, Bünyamin
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Akguel, B
Akgül, B.
Akgul, B.
Akgül, A.
Akguel, Buenyamin
Akgul, Buenyamin
Akguel, B.
Akgul, Bunyamin
Akgül, B.
Akgul, B.
Akgül, A.
Akguel, Buenyamin
Akgul, Buenyamin
Akguel, B.
Akgul, Bunyamin
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Email Address
bunyaminakgul@iyte.edu.tr
Main Affiliation
04.03. Department of Molecular Biology and Genetics
Status
Current Staff
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WoS Researcher ID
Sustainable Development Goals
1NO POVERTY
0
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2ZERO HUNGER
1
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3GOOD HEALTH AND WELL-BEING
23
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4QUALITY EDUCATION
2
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5GENDER EQUALITY
1
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6CLEAN WATER AND SANITATION
0
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7AFFORDABLE AND CLEAN ENERGY
0
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8DECENT WORK AND ECONOMIC GROWTH
0
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9INDUSTRY, INNOVATION AND INFRASTRUCTURE
6
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10REDUCED INEQUALITIES
0
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11SUSTAINABLE CITIES AND COMMUNITIES
0
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12RESPONSIBLE CONSUMPTION AND PRODUCTION
0
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13CLIMATE ACTION
0
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14LIFE BELOW WATER
0
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15LIFE ON LAND
0
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16PEACE, JUSTICE AND STRONG INSTITUTIONS
1
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17PARTNERSHIPS FOR THE GOALS
0
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Documents
37
Citations
483
h-index
11
Documents
31
Citations
312
Scholarly Output
69
Articles
32
Views / Downloads
210361/23978
Supervised MSc Theses
20
Supervised PhD Theses
3
WoS Citation Count
209
Scopus Citation Count
344
Patents
0
Projects
25
WoS Citations per Publication
3.03
Scopus Citations per Publication
4.99
Open Access Source
49
Supervised Theses
23
| Journal | Count |
|---|---|
| Turkish Journal of Biology | 7 |
| Methods in Molecular Biology | 5 |
| PLoS ONE | 3 |
| FASEB Journal | 2 |
| Journal of Cellular Physiology | 2 |
Current Page: 1 / 5
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69 results
Scholarly Output Search Results
Now showing 1 - 10 of 69
Article Citation - WoS: 5Citation - Scopus: 7Re-Arrangements in the Cytoplasmic Distribution of Small Rnas Following the Maternal-To Transition in Drosophila Embryos(MDPI Multidisciplinary Digital Publishing Institute, 2018) Coşacak, Mehmet İlyas; Yiğit, Hatice; Kızıl, Çağhan; Akgül, BünyaminSmall ribonucleic acids (RNAs) are known to regulate gene expression during early development. However, the dynamics of interaction between small RNAs and polysomes during this process is largely unknown. To investigate this phenomenon, 0-1 h and 7-8 h Drosophila melanogaster embryos were fractionated on sucrose density gradients into four fractions based on A254 reading (1) translationally inactive messenger ribonucleoprotein (mRNP), (2) 60S, (3) monosome, and (4) polysome. Comparative analysis of deep-sequencing reads from fractionated and un-fractionated 0-1 h and 7-8 h embryos revealed development-specific co-sedimentation pattern of small RNAs with the cellular translation machinery. Although most micro RNAs (miRNAs) did not have a specific preference for any state of the translational machinery, we detected fraction-specific enrichment of a few miRNAs such as dme-miR-1-3p, -184-3p, 5-5p and 263-5p. More interestingly, we observed changes in the subcellular location of a subset of miRNAs in fractionated embryos despite no measurable difference in their amount in unfractionated embryos. Transposon-derived endo small interfering RNAs (siRNAs) were over-expressed in 7-8 h embryos and associated mainly with the mRNP fraction. In contrast, transposon-derived PIWI-interacting RNAs (piRNA), which were more abundant in 0-1 h embryos, co-sedimented primarily with the polysome fractions. These results suggest that there appears to be a complex interplay among the small RNAs with respect to their polysome-cosedimentation pattern during early development in Drosophila melanogaster.Article Citation - WoS: 3Citation - Scopus: 3Regulation of Mrna Stability Through a Pentobarbital-Responsive Element(Elsevier Ltd., 2007) Akgül, Bünyamin; Tu, Chen-Pei D.Pentobarbital, a general anesthetic and non-genotoxic carcinogen, can induce gene expression by activating transcription. In the Drosophila glutathione S-transferase D21 (gstD21) gene, pentobarbital's regulatory influence extends to the level of mRNA turnover. Transcribed from an intronless gene, gstD21 mRNA is intrinsically very labile. But exposure to pentobarbital renders it stabilized beyond what can be attributed to transcriptional activation. We aim here to identify cis-acting element(s) of gstD21 mRNA as contributors to the molecule's pentobarbital-mediated stabilization. In the context of hsp70 5′UTR and the 3′UTR of act5C, gstD21 mRNA, minus its native UTRs, is stable. Maintaining the same context of heterologous UTRs, we can reconstitute using the full-length gstD21 sequence the inherent instability of gstD21 mRNA and its stabilization by pentobarbital. Transgenic flies that express these chimeric gstD21 mRNA exhibit decay intermediates lacking 3′UTR, which are not stabilized by PB treatment. The 3′UTR sequence, when inserted downstream from a reporter transcript, stabilizes it 1.6-fold under PB treatment. The analysis of the decay intermediates suggests a polysome-associated decay pattern. We propose a regulatory model that features a 59-nucleotide pentobarbital-responsive element (PBRE) in the 3′UTR of gstD21 mRNA.Conference Object Expression Profiling of a Novel Intronic RNA and Its Potential Interactions With miRNAs(Wiley, 2025) Ceren, S. E.; Gurer, D. C.; Vatansever, I. Erdogan; Akkas, N. S.; Karaca, U.; Akgul, B.Conference Object Dietary Garlic Prevents Development of Diabesity in Mice(FASEB, 2009) Tu, Chen-Pei David; Akgül, Bünyamin; Lin, Kai-Wei; Pan, Huei-Ju; Chen, Yen-Hui; Lu, Tzu-Huan; Chen, Yuan-Tsong[No abstract available]Conference Object The Importance of Mirna Expressions in Infertilty(Wiley, 2016) Gökalp, S.; Akgül, Bünyamin; Özçakır, T.; Vatansever, H. S.Implantation process is controlled with endometrium, factors secreted by the embryos and in accordance with these factors embryo and/or endometrium via receptors on. More than 700 human MicroRNA (miRNAs) that are small noncoding RNAs were shown to play an important role in intracelluler cycle regulation in both normal and pathological conditions. In this study we aim to identify miRNAs and controlling molecules expressions in different time period of endometrium in fertile and infertile cases.Article Citation - WoS: 6Epitranscriptomics M<sup>6</Sup>a Analyses Reveal Distinct M<sup>6</Sup>a Marks Under Tumor Necrosis Factor Α (tnf-Α) Apoptotic Conditions in Hela Cells(Wiley, 2024) Akçaöz Alasar, Azime; Tüncel, Özge; Sağlam, Buket; Gazaloğlu, Yasemin; Atbinek, Melis; Çağıral, Umut; Akgül, BünyaminTumor necrosis factor-alpha (TNF-alpha) is a ligand that induces both intrinsic and extrinsic apoptotic pathways in HeLa cells by modulating complex gene regulatory mechanisms. However, the full spectrum of TNF-alpha-modulated epitranscriptomic m(6)A marks is unknown. We employed a genomewide approach to examine the extent of m(6)A RNA modifications under TNF-alpha-modulated apoptotic conditions in HeLa cells. miCLIP-seq analyses revealed a plethora of m(6)A marks on 632 target mRNAs with an enrichment on 99 mRNAs associated with apoptosis. Interestingly, the m(6)A RNA modification patterns were quite different under cisplatin- and TNF-alpha-mediated apoptotic conditions. We then examined the abundance and translational efficiencies of several mRNAs under METTL3 knockdown and/or TNF-alpha treatment conditions. Our analyses showed changes in the translational efficiency of TP53INP1 mRNA based on the polysome profile analyses. Additionally, TP53INP1 protein amount was modulated by METTL3 knockdown upon TNF-alpha treatment but not CP treatment, suggesting the existence of a pathway-specific METTL3-TP53INP1 axis. Congruently, METLL3 knockdown sensitized HeLa cells to TNF-alpha-mediated apoptosis, which was also validated in a zebrafish larval xenograft model. These results suggest that apoptotic pathway-specific m(6)A methylation marks exist in cells and TNF-alpha-METTL3-TP53INP1 axis modulates TNF-alpha-mediated apoptosis in HeLa cells.Article Citation - WoS: 13Citation - Scopus: 13Differentially Expressed Trna-Derived Small Rnas Co-Sediment Primarily With Non-Polysomal Fractions in Drosophila(MDPI Multidisciplinary Digital Publishing Institute, 2017) Göktaş, Çağdaş; Yiğit, Hatice; Coşacak, Mehmet İlyas; Akgül, BünyaminRecent studies point to the existence of poorly characterized small regulatory RNAs generated from mRNAs, rRNAs and tRNAs. To explore the subcellular location of tRNA-derived small RNAs, 0–1 and 7–8 h Drosophila embryos were fractionated on sucrose density gradients. Analysis of 12,553,921 deep-sequencing reads from unfractionated and fractionated Drosophila embryos has revealed that tRFs, which are detected mainly from the 5’ends of tRNAs, co-sediment with the non-polysomal fractions. Interestingly, the expression levels of a subset of tRFs change temporally following thematernal-to-zygotic transition in embryos. We detected non-polysomal association of tRFs in S2 cells as well. Differential tRF expression pattern points to developmental significance at the organismal level. These results suggest that tRFs are associated primarily with the non-polysomal complexes in Drosophila embryos and S2 cells.Master Thesis Examination of Stable Intronic Sequence Rna Profile Under Apoptotic Conditions(Izmir Institute of Technology, 2022) Kara, Merve; Akgül, BünyaminApoptosis is a process of programmed cell death. Cisplatin, a chemotherapeutic drug, activates intrinsic pathway of apoptosis while TNF-alpha, a death ligand, activates the extrinsic pathway of apoptosis. Noncoding RNAs involve in regulation of apoptotic pathways at post-transcriptional level. Stable intronic sequence RNAs (sisRNAs) are the novel class of non-coding RNAs which can be generated by splicing- dependent and independent mechanisms. sisRNAs transcribed from their intronic promoter may contain 5’ cap and polyA tail. Despite the reports of several studies about sisRNAs in Xenopus and Drosophila, a genome-wide profile of sisRNAs in human is lacking. Therefore, we aimed to identify sisRNAs profile that are transcribed from their intronic promoter under cisplatin- and TNF-alpha- mediated apoptosis conditions. In this thesis study, the deep sequencing of total RNA, polyA + and polyA eliminated fractions from cisplatin-, TNFalpha-, DMSO-treated cells were performed. Differentially expressed intronic transcripts were analysed by DE-kupl algorithm. The intronic transcripts both in total RNA and polyA + RNA fractions but not in polyA eliminated fractions were screened visually on Integrated Genome Viewer (IGV) and selected as sisRNA candidateS. 48 sisRNA candidates were detected in cisplatin-treated data while 33 sisRNA candidates were detected in TNF-alpha- treated data. 5’ and 3’ RACE PCRs were performed for determination of transcriptional units of sisRNA candidates. Overexpression of sisRDOCK7-IT1 caused 8.09% increase in total apoptosis of HeLa cells in 48 hours. sisRDOCK7-IT1 triggers the activation of apoptosis but the mechanism of its induction of apoptosis is still unknown.Article Citation - WoS: 10Citation - Scopus: 14Garlic Accelerates Red Blood Cell Turnover and Splenic Erythropoietic Gene Expression in Mice: Evidence for Erythropoietin-Independent Erythropoiesis(Public Library of Science, 2010) Akgül, Bünyamin; Lin, Kai-Wei; Yang, Hui-Mei Ou; Chen, Yen-Hui; Lu, Tzu-Huan; Chen, Chien-Hsiun; Kikuchi, Tateki; Chen, Yuan-Tsong; Tu, Chen-Pei D.Garlic (Allium sativum) has been valued in many cultures both for its health effects and as a culinary flavor enhancer. Garlic's chemical complexity is widely thought to be the source of its many health benefits, which include, but are not limited to, anti-platelet, procirculatory, anti-inflammatory, anti-apoptotic, neuro-protective, and anti-cancer effects. While a growing body of scientific evidence strongly upholds the herb's broad and potent capacity to influence health, the common mechanisms underlying these diverse effects remain disjointed and relatively poorly understood. We adopted a phenotypedriven approach to investigate the effects of garlic in a mouse model. We examined RBC indices and morphologies, spleen histochemistry, RBC half-lives and gene expression profiles, followed up by qPCR and immunoblot validation. The RBCs of garlic-fed mice register shorter half-lives than the control. But they have normal blood chemistry and RBC indices. Their spleens manifest increased heme oxygenase 1, higher levels of iron and bilirubin, and presumably higher CO, a pleiotropic gasotransmitter. Heat shock genes and those critical for erythropoiesis are elevated in spleens but not in bone marrow. The garlic-fed mice have lower plasma erythropoietin than the controls, however. Chronic exposure to CO of mice on garlic-free diet was sufficient to cause increased RBC indices but again with a lower plasma erythropoietin level than air-treated controls. Furthermore, dietary garlic supplementation and CO treatment showed additive effects on reducing plasma erythropoietin levels in mice. Thus, garlic consumption not only causes increased energy demand from the faster RBC turnover but also increases the production of CO, which in turn stimulates splenic erythropoiesis by an erythropoietinindependent mechanism, thus completing the sequence of feedback regulation for RBC metabolism. Being a pleiotropic gasotransmitter, CO may be a second messenger for garlic's other physiological effects.Master Thesis Investigation of the Effect of Dr5-As Long Non-Coding Rna on Cell Proliferation(Izmir Institute of Technology, 2020) Gürer, Dilek Cansu; Akgül, BünyaminCell proliferation is the process of increasing cell number in a multicellular organism. In literature, there are numerous proteins and non-coding RNAs reported as regulators of cell proliferation, yet, many of others are waiting to be explored. Unravelling the mechanism behind the regulation of cell proliferation is crucial to develop new strategies for fighting numerous diseases such as cancer, immune diseases, or neurodegenerative diseases. Long non-coding RNAs (lncRNAs) are known to regulate various cellular processes. To determine which ones are related to cell proliferation and apoptosis in HeLa cells, a transcriptomics study was performed under cisplatin, doxorubicin, TNF-? and Anti-Fas treatments. DR5-AS is a novel lncRNA transcript selected from this transcriptomics study as a promising regulatory lncRNA candidate due to its overlap with DR5 protein-coding gene which is known to regulate apoptosis and proliferation. Several phenotypic characterization methods were performed to understand the function of DR5-AS lncRNA. These studies showed that DR5-AS knockdown causes a significant decrease in cell proliferation, an alteration in the normal HeLa cell morphology, a shift through S and G2/M phases in cell cycle profile, and significant accumulation of cells in the metaphase phase. A second transcriptomics study was performed with DR5-AS knockdown HeLa cells to uncover which pathways are responsible for these changes. The results suggest that DR5-AS lncRNA regulates expression of numerous key proteins in cell cycle regulation. This observation was confirmed by several qPCR experiments. In conclusion, this study provides the first evidence that DR5-AS lncRNA modulates cell cycle and proliferation in HeLa cells.