Akgül, Bünyamin
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Akgul, Bunyamin
Akgül, Bünyamin
Akgül,B.
Akgul,B.
Akgül, Bünyamin
Akgül,B.
Akgul,B.
Job Title
Prof. Dr.
Email Address
bunyaminakgul@iyte.edu.tr
Main Affiliation
Moleküler Biyoloji ve Genetik Bölümü
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Sustainable Development Goals
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Scholarly Output
33
Articles
18
Citation Count
0
Supervised Theses
1
31 results
Scholarly Output Search Results
Now showing 1 - 10 of 31
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.; 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) Yaylak,B.; 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 Knockdown of death receptor 5 antisense long noncoding RNA and cisplatin treatment modulate similar macromolecular and metabolic changes in HeLa cells(Tubitak Scientific & Technological Research Council Turkey, 2022) Gurer, Dilek Cansu; Erdogan Vatansever, Ipek; Ceylan, Cagatay; Akgul, BunyaminBackground/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.Master Thesis Isothermal corrosion testing of frit furnace refractories(Izmir Institute of Technology, 2008) Balıkoğlu, Fatih; 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.Review Intracytoplasmic Re-localization of miRISC Complexes(Frontiers Media Sa, 2018) Akgul, Bunyamin; Erdogan, IpekMicroRNAs (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.Article Transcriptomics Analysis of Circular RNAs Differentially Expressed in Apoptotic HeLa Cells(Frontiers Media Sa, 2019) Yaylak, Bilge; Erdogan, Ipek; Akgul, BunyaminApoptosis is a form of regulated cell death that plays a critical role in survival and developmental homeostasis. There are numerous reports on regulation of apoptosis by protein-coding genes as well as small non-coding RNAs, such as microRNAs. However, there is no comprehensive investigation of circular RNAs (circRNA) that are differentially expressed under apoptotic conditions. We have performed a transcriptomics study in which we first triggered apoptosis in HeLa cells through treatment with four different agents, namely cisplatin, doxorubicin, TNF-alpha and anti-Fas mAb. Total RNAs isolated from control as well as treated cells were treated with RNAse R to eliminate the linear RNAs. The remaining RNAs were then subjected to deep-sequencing to identify differentially expressed circRNAs. Interestingly, some of the dys-regulated circRNAs were found to originate from protein-coding genes well-documented to regulate apoptosis. A number of candidate circRNAs were validated with qPCR with or without RNAse R treatment as well. We then took advantage of bioinformatics tools to investigate the coding potential of differentially expressed RNAs. Additionally, we examined the candidate circRNAs for the putative miRNA-binding sites and their putative target mRNAs. Our analyses point to a potential for circRNA-mediated sponging of miRNAs known to regulate apoptosis. In conclusion, this is the first transcriptomics study that provides a complete circRNA profile of apoptotic cells that might shed light onto the potential role of circRNAs in apoptosis.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, AytenOne 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 Regulation of mRNA stability through a pentobarbital-responsive element(Elsevier Science inc, 2007) Akgul, Bunyamin; 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. (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, BunyaminApoptosis 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[No Abstract Available]
