Akgül, Bünyamin
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Akgul, Bunyamin
Akgül, Bünyamin
Akgül,B.
Akgul,B.
Akgül, Bünyamin
Akgül,B.
Akgul,B.
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Prof. Dr.
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bunyaminakgul@iyte.edu.tr
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Moleküler Biyoloji ve Genetik Bölümü
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31 results
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Master Thesis Isothermal corrosion testing of frit furnace refractories(Izmir Institute of Technology, 2008) Balıkoğlu, Fatih; Akgül, Bünyamin; Akkurt, SedatResults of a project aimed at understanding the corrosion behavior of aluminosilicate type of refractories in frit melts are presented. A refractory of largely andalusite and silimanite composition was compared to another brick of mullite and silimanite composition which was made by a different manufacturer for use in a different frit furnace. Density, porosity, microstructure and chemistry of both bricks are characterized before the corrosion tests. Isothermal tests were conducted by partially immersing a 15x15x115mm square specimen into a frit melt between 1404 and 1504oC in a vertical tube furnace. The frit used had an industrially used transparent frit composition. The effects of temperature, duration of exposure and refractory type were investigated using a statistically designed set of experiments. The ANOVA (Analysis of variance) table indicated that temperature and duration were more important factor effects. Increasing exposure duration and temperature both led to increased amount of corrosion as measured by the cross sectional area loss of the corroded specimen.Postmortem microstructural analysis was also done on the specimens and extensive amount of ZnO.Al2O3 precipitation was observed along the frit-refractory interface where also other crystals of mullite and alumina were found to precipitate. Increasing amount of duration and temperature produced more ZnO.Al2O3 precipitation. As identified by SEM-EDS analysis, mullite cyrstals were in the needle like morphology while alumina crystals were generally cubic. Because of their small concentration, XRD analysis could not reveal the phases of these crystals. More experiments were done by rotating the specimens in the melt at 50 rpm of rotational speed. Due to the reduction of boundary layer thickness, more dissolution was observed from the rotated specimens. In all specimens corrosion was more pronounced in the bond phase than through the large filler grains of mullite and andalusite.Keywords: Refractories, frit, corrosion, test.Article Aggregatibacter actinomycetemcomitans GroEL Protein Promotes Conversion of Human CD4+T Cells into IFNγ IL10 Producing Tbet+Th1 Cells(Public Library Science, 2012) Saygili, Tahsin; Akincilar, Semih Can; Akgul, Bunyamin; Nalbant, Ayten; Akgül, BünyaminOne of the heat shock family protein (Hsp) expressing bacteria is the gram negative, periodontal pathogen Aggregatibacter actinomycetemcomitans (Aa). A. actinomycetemcomitans' Hsp is a 64-kDa GroEL-protein, which has been shown to influence the host cells. In this study we used recombinant A. actinomycetemcomitans GroEL (rAaGroEL) protein as a model antigen to study GroEL-mediated T cell immune response. Human peripheral mononuclear cells (PBMCs), when stimulated with recombinant rAaGroEL, expressed early activation marker CD69 and IL-2R (CD25). CD25 and CD69 expressions were higher in CD4+ T cells compared to CD8+ T cells. rAaGroEL-responding CD4+ T cells expressed IL-10, IFN gamma and TNF alpha cytokines. Interestingly, there were also IL-10 and IFN gamma double cytokine producing CD4+ T cells. Additionally, IFN gamma expressing CD4+ T cells were also T-bet positive. Altogether the results suggest that rAaGroEL protein affects CD4+ T cells to differentiate into IFN gamma IL10-secreting T-bet+ Th1 cells.Article Knockdown of death receptor 5 antisense long noncoding RNA and cisplatin treatment modulate similar macromolecular and metabolic changes in HeLa cells(TUBITAK, 2022) Gürer,D.C.; Akgül, Bünyamin; Erdoğan Vatansever,İ.; Ceylan,Ç.; Akgül,B.Background/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 ametabolic changes in HeLa cervix cancer cells. © TÜBİTAK.Book Part Experimental MicroRNA Detection Methods(Humana Press Inc., 2022) Akgül, Bünyamin; Akgül,B.MicroRNAs (miRNAs) are considerably small yet highly important riboregulators involved in nearly all cellular processes. Due to their critical roles in posttranscriptional regulation of gene expression, they have the potential to be used as biomarkers in addition to their use as drug targets. Although computational approaches speed up the initial genomewide identification of putative miRNAs, experimental approaches are essential for further validation and functional analyses of differentially expressed miRNAs. Therefore, sensitive, specific, and cost-effective microRNA detection methods are imperative for both individual and multiplex analysis of miRNA expression in different tissues and during different developmental stages. There are a number of well-established miRNA detection methods that can be exploited depending on the comprehensiveness of the study (individual miRNA versus multiplex analysis), the availability of the sample and the location and intracellular concentration of miRNAs. This review aims to highlight not only traditional but also novel strategies that are widely used in experimental identification and quantification of microRNAs. © 2022, Springer Science+Business Media, LLC, part of Springer Nature.Article Regulation of mRNA stability through a pentobarbital-responsive element(Elsevier Science inc, 2007) Akgul, Bunyamin; Tu, Chen-Pei D.; Akgül, BünyaminPentobarbital, 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. (c) 2006 Elsevier Inc. All rights reserved.Review Noncoding RNAs in apoptosis: identification and function(Tubitak Scientific & Technological Research Council Turkey, 2022) Tuncel, Ozge; Kara, Merve; Yaylak, Bilge; Erdogan, Ipek; Akgul, Bunyamin; 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.Conference Object Dietary Garlic Prevents Development of Diabesity in Mice(Federation Amer Soc Exp Biol, 2009) Tu, Chen-Pei David; Akgul, Bunyamin; Lin, Kai-Wei; Pan, Huei-Ju; Chen, Yen-Hui; Lu, Tzu-Huan; Chen, Yuan-Tsong; Akgül, Bünyamin[No Abstract Available]Article Genomewide m6A Mapping Uncovers Dynamic Changes in the m6A Epitranscriptome of Cisplatin-Treated Apoptotic HeLa Cells(Mdpi, 2022) Alasar, Azime Akcaoz; Tuncel, Ozge; Gelmez, Ayse Bengisu; Saglam, Buket; Vatansever, Ipek Erdogan; Akgul, Bunyamin; 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 m(6)A methylome are unknown. We employed an m(6)A miCLIP-seq approach to investigate the effect of m(6)A methylation marks under cisplatin-mediated apoptotic conditions on HeLa cells. Our high-resolution approach revealed numerous m(6)A 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 m(6)A methylation events and that the METTL3-PMAIP1 axis modulates cisplatin-mediated apoptosis in HeLa cells.Article Genomewide m6A Mapping Uncovers Dynamic Changes in the m6A Epitranscriptome of Cisplatin-Treated Apoptotic HeLa Cells(MDPI, 2022) Alasar,A.A.; Akgül, Bünyamin; Tüncel,Ö.; Gelmez,A.B.; Sağlam,B.; Vatansever,İ.E.; Akgül,B.Cisplatin (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. © 2022 by the authors.Data Paper Small RNA data set that includes tRNA-derived fragments from Jurkat cells treated with camptothecin(Elsevier Ltd., 2018-04) Coşacak, Mehmet İlyas; Akgül, Bünyamin; Erdoğan, İpek; Nalbant, Ayten; Akgül, BünyaminIn this article, we report a small RNA data set obtained from human T cell acute leukemia Jurkat cells, which were treated with the universal apoptotic agent camptothecin. Based on the Annexin-V labeling pattern, we sorted two Jurkat subpopulations in treated cells: one that is sensitive to the drug and the other being relatively more resistant. We report new original data that include the frequency of tRNA-derived fragments (tRF) in drug-sensitive and resistant cells. We also present partially analyzed data to show the origin of reads on tRNAs as well as the borders of the fragments. We believe that this data can benefit the science community working in the field of tRF and/or apoptosis.
