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Recent Submitted Publications
Investigation of interlayer hybridization effect on burst pressure performance of composite overwrapped pressure vessels with load-sharing metallic liner
(Sage Publications Ltd, 2020) Kangal, Serkan; Kartav, Osman; Tanoglu, Metin; Aktas, Engin; Artem, H. Secil; Tanoğlu, Metin
In this study, multi-layered composite overwrapped pressure vessels for high-pressure gaseous storage were designed, modeled by finite element method and manufactured by filament winding technique. 34CrMo4 steel was selected as a load-sharing metallic liner. Glass and carbon filaments were overwrapped on the liner with a winding angle of [+/- 11 degrees/90 degrees(2)](3) to obtain fully overwrapped composite reinforced vessel with non-identical front and back dome endings. The vessels were loaded with increasing internal pressure up to the burst pressure level. The mechanical performances of pressure vessels, (i) fully overwrapped with glass fibers and (ii) with additional two carbon hoop layers on the cylindrical section, were investigated by both experimental and numerical approaches. In numerical approaches, finite element analysis was performed featuring a simple progressive damage model available in ANSYS software package for the composite section. The metal liner was modeled as elastic-plastic material. The results reveal that the finite element model provides a good correlation between experimental and numerical strain results for the vessels, together with the indication of the positive effect on radial deformation of the COPVs due to the composite interlayer hybridization. The constructed model was also able to predict experimental burst pressures within a range of 8%. However, the experimental and finite element analysis results showed that hybridization of hoop layers did not have any significant impact on the burst pressure performance of the vessels. This finding was attributed to the change of load-sharing capacity of composite layers due to the stiffness difference of carbon and glass fibers.
Cytoplasmically localized tRNA-derived fragments inhibit translation in Drosophila S2 cells
(TUBITAK, 2022) Hamid,S.M.; Akgül,B.; Moleküler Biyoloji ve Genetik Bölümü; Moleküler Biyoloji ve Genetik Bölümü
Transfer ribonucleic acids (tRNAs) serve not only as amino acid carriers during translation but also as a template for the biogenesis of short fragments that can regulate gene expression. Despite recent progress in the function of tRNA-derived fragments (tRFs), their intracellular localization, protein partners, and role in regulating translation are not well understood. We used synthetic tRFs to investigate their localization and function in Drosophila S2 cells. Under our experimental setting, all synthetic tRFs tested were localized at distinct sites within the cytoplasm in a similar manner in Drosophila S2 cells. Cytoplasmically-localized tRFs were positioned in close proximity to GW182 and XRN1 proteins. Functionally, tRFs, which slightly suppressed proliferation in S2 cells, inhibited translation without any major shift in the polysome profile. These results suggest that 5’-tRFs are cytoplasmically-localized and regulate gene expression through inhibition of translation in Drosophila. © TÜBİTAK.
Endogenous heat shock protein GroEL of A. actinomycetemcomitans preferentially targets primary human CD8+ T cells
(2015) Aldanmaz Nalbant, AYTEN; Akgül, Bünyamin; Kant, Melis
Apoptosis can be used to manipulate host cells by bacterial products such as bacterial heat shock proteins (Hsp). One of the virulence factors of periodontal pathogen Aggregatibacter actinomycetemcomitans is heat shock protein GroEL (AaGroEL), which has been shown to interact with host cells. AaGroEL (Hsp64) also has the potential to modulate immune system cells. In this study we used endogenous AaGroEL protein as an antigen to study bacterial Hsp-induced apoptosis in different immune system cells. Human peripheral blood mononuclear cells and cell lines were cultured with different doses (50-1000 ng/mL) of endogenous AaGroEL at various time points. Apoptosis of the cells was measured by Annexin V and 7AAD labeling. Apoptotic cells were analyzed by flow cytometry. Our data suggested that AaGroEL-responding primary CD8+ T cells were more susceptible to apoptosis than CD4+ T cells. Furthermore, the magnitude of apoptosis in the Jurkat T cell line was higher than that in primary CD8+ T cells. There was no statistically significant level of apoptosis in the chronic myeloid leukemia (K562) cell line, which belongs to myeloid lineages. Thus, A. actinomycetemcomitans GroEL protein has more potent apoptotic effect on cells that are derived from a lymphoid progenitor.
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.
Genomewide m6A Mapping Uncovers Dynamic Changes in the m6A Epitranscriptome of Cisplatin-Treated Apoptotic HeLa Cells
(MDPI, 2022) Alasar,A.A.; 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.