TR Dizin İndeksli Yayınlar / TR Dizin Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/11147/7149
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Article Citation - WoS: 4Citation - Scopus: 3Expression Patterns of M6a Rna Methylation Regulators Under Apoptotic Conditions in Various Human Cancer Cell Lines(TUBITAK, 2024) Alasar, Azime Akçaöz; Sağlam, Buket; Vatansever, İpek Erdoğan; Akgül, BünyaminBackground/aim: Cancer is a complex disease that involves both genetic and epigenetic factors. While emerging evidence clearly suggests that changes in epitranscriptomics play a crucial role in cancer pathogenesis, a comprehensive understanding of the writers, erasers, and readers of epitranscriptomic processes, particularly under apoptotic conditions remains lacking. The aim of this study was to uncover the changes in the expression of m6A RNA modifiers under apoptotic conditions across various cancer cell lines. Materials and methods: Initially, we quantified the abundance of m6A RNA modifiers in cervical (HeLa and ME180), breast (MCF7 and MDA-MB-231), lung (A549 and H1299), and colon (Caco-2 and HCT116) cancer cell lines using qPCR. Subsequently, we induced apoptosis using cisplatin and tumor necrosis factor-alpha (TNF-α) to activate intrinsic and extrinsic pathways, respectively, and assessed apoptosis rates via flow cytometry. Further, we examined the transcript abundance of m6A RNA modifiers under apoptotic conditions in cervical, breast, and lung cancer cell lines using qPCR. Results: Overall, treatment with cisplatin increased the abundance of m 6A modifiers, whereas TNF-α treatment decreased their expression in cervical, breast, and lung cancer cell lines. Specifically, cisplatin-induced apoptosis, but not TNF-α-mediated apoptosis, resulted in decreased abundance of METTL14 and FTO transcripts. Additionally, cisplatin treatment drastically reduced the abundance of IGF2BP2 and IGF2BP3 readers. Conclusion: These results suggest that the differential response of cancer cells to apoptotic inducers may be partially attributed to the expression of m6A RNA modifiers.Article Citation - WoS: 2Citation - Scopus: 1A Review of the Geothermal System Evolution and Distribution in the Central Anatolian Crystalline Complex (türkiye)(TUBITAK, 2023) Şener, M.F.; Öztürk, M.Z.; Baba, A.Türkiye is located in the Mediterranean sector of the Alpine–Himalayan tectonic belt and is among the foremost seven countries in the world having an abundance of geothermal resources. The Central Anatolian Crystalline Complex (CACC) is one of the most important geothermal regions in Türkiye. This study aims to evaluate the geothermal system of CACC using the geological, structural, and hydrogeochemical properties that were obtained from previous studies. The present study investigated and evaluated the hydrogeochemical and isotopic properties of 762 water samples belonging to 45 different localities from 41 scientific studies. The result shows that CACC has different heat sources and different hydrogeochemical processes. Major element chemistry of the water reveals that the geothermal fluids are mostly of the Ca-Mg-HCO3, Na-Cl-HCO3, and Ca-Cl water types. Silica geothermometers suggest that the reservoir temperature ranges from 48 to 180 °C. Based on the δ18O-δD relationship, water samples have a high-altitude meteoric origin. Stable isotopic data indicate that the geothermal fluids are formed by local recharge and deep circulation of meteoric waters. © TÜBİTAK.Article Citation - WoS: 28Citation - Scopus: 30Bone Marrow Stem Cells Adapt To Low-Magnitude Vibrations by Altering Their Cytoskeleton During Quiescence and Osteogenesis(TUBITAK, 2015) Demiray, Levent; Özçivici, EnginApplication of mechanical vibrations is anabolic to bone tissue, not only by guiding mature bone cells to increased formation, but also by increasing the osteogenic commitment of progenitor cells. However, the sensitivity and adaptive response of bone marrow stem cells to this loading regimen has not yet been identified. In this study, we subjected mouse bone marrow stem cell line D1-ORL-UVA to daily mechanical vibrations (0.15 g, 90 Hz, 15 min/day) for 7 days, both during quiescence and osteogenic commitment, to identify corresponding ultrastructural adaptations on cellular and molecular levels. During quiescence, mechanical vibrations significantly increased total actin content and actin fiber thickness, as measured by phalloidin staining and fluorescent microscopy. Cellular height also increased, as measured by atomic force microscopy, along with the expression of focal adhesion kinase (PTK2) mRNA levels. During osteogenesis, mechanical vibrations increased the total actin content, actin fiber thickness, and cytoplasmic membrane roughness, with significant increase in Runx2 mRNA levels. These results show that bone marrow stem cells demonstrate similar cytoskeletal adaptations to low-magnitude high-frequency mechanical loads both during quiescence and osteogenesis, potentially becoming more sensitive to additional loads by increased structural stiffness.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: 4Citation - Scopus: 4PEG-peptide conjugate containing cathepsin B degradation unit as a doxorubicin carrier system(TUBITAK, 2018) Şentürk, Nesligül; Top, AybenA drug delivery system (DDS) containing a cathepsin B degradable sequence and pH-responsive histidines was prepared by methoxypolyethylene glycol and peptide conjugation. Doxorubicin was attached to the carrier system using amide linkage to give the final form of the DDS, denoted as mPEG-AT3-DOX. mPEG-AT3-DOX exhibited a bimodal size distribution at about 15 and 30 nm independent of pH, whereas the size of the control DDS containing no peptide sequence, mPEG-DOX, was measured as ∼ 15–20 nm. At the end of 72 h, % doxorubicin release from both of the DDSs was observed to be below 8.5 ± 3% in the absence of cathepsin B, and it increased to 17 ± 2% in the presence of cathepsin B for mPEG-AT3-DOX. Complete degradation of AT3 peptide within 3 h upon incubation with cathepsin B suggests that lower than expected doxorubicin release is likely due to the aggregation tendency of mPEG-AT3-DOX. Absolute IC50 values indicated that the cytotoxicity trend of the samples is in the order of free DOX ≥ mPEG-AT3-DOX >mPEG-DOX. Considering these results, PEG-peptide-doxorubicin conjugates can be promising candidates in cancer therapy if they are designed to have more pronounced pH-responsive behavior to increase the drug release rate.Article Citation - WoS: 1Citation - Scopus: 1Comparative Proteomic Analysis of Bacillus Thuringiensis Wild-Type and Two Mutant Strains Disturbed in Polyphosphate Homeostasis(TUBITAK, 2018) Yeşilırmak, Filiz; Doruk, Tuğrul; Yılmaz, Şerif; Tunca Gedik, SedefPolyphosphate polymer (polyP) plays a very important role in every living cell. Synthesis of this linear polymer of phosphate (Pi) residues is catalyzed by the polyphosphate kinase (PPK) enzyme. It was shown that high levels of intracellular polyphosphate stimulated endotoxin production by Bacillus thuringiensis subsp. israelensis (Bti). In this study, proteomic analysis of the wild-type and two mutant strains, overexpressing the ppk gene (Bti pHTppk) and without the ppk gene (Bti ∆ppk), were used to clarify the relation between polyP and endotoxin production. Intracellular proteins were separated by two-dimensional gel electrophoresis; 41 spots of interest (proteins differentially expressed) were obtained and 35 of them were identified by mass spectrometry. Analysis of the protein profiles showed that there is a general decrease in the expression levels of proteins related with energy metabolism, amino acid metabolism, and purine biosynthesis in both Bti pHTppk and Bti ∆ppk. Gluconeogenesis and fatty acid metabolism were also slowed down in both strains, whereas expression of stress response proteins increased compared to the wild-type. These results suggested that changes in polyP concentration cause a general stress condition inside the cell, which in turn stimulates secondary metabolite synthesisArticle Citation - WoS: 8Citation - Scopus: 13Anticorrosion Coating for Magnesium Alloys: Electrospun Superhydrophobic Polystyrene/Sio2 Composite Fibers(TUBITAK, 2018) Horzum Polat, Nesrin; Kap, Özlem; Farzaneh, AmirSuperhydrophobic nanocomposite coatings for magnesium surfaces with remarkable corrosion resistance were fabricated by electrospinning in the presence of fluorosilane-functionalized silica (SiO2) nanoparticles. The effects of surface-modified silica (mod-SiO2) nanoparticles on the superhydrophobicity and corrosion resistance of polystyrene (PS)/mod-SiO2 fiber coatings were evaluated. The incorporation of the SiO2 nanoparticles endows PS fibers with rough surfaces exhibiting a water contact angle (WCA) of 165◦. The surface wettability, corrosion resistance, and their relation to the inorganic content in the PS fibers and the contact angle of the composite coatings were explored. Analysis of the corrosion results confirmed that the PS/mod-SiO2 coating protected the Mg surface from corrosion. In addition, PS fibers containing mod-SiO2 nanoparticles showed improved hydrophobicity, and excellent corrosion resistance was achieved with PS fibers containing 4 wt% SiO2 nanoparticles.Article Citation - WoS: 5Citation - Scopus: 5Convergence Analysis and Numerical Solution of the Benjamin-Bona Equation by Lie-Trotter Splitting(TUBITAK, 2018) Zürnacı, Fatma; Gücüyenen Kaymak, Nurcan; Seydaoğlu, Muaz; Tanoğlu, GamzeIn this paper, an operator splitting method is used to analyze nonlinear Benjamin-Bona-Mahony-type equations. We split the equation into an unbounded linear part and a bounded nonlinear part and then Lie-Trotter splitting is applied to the equation. The local error bounds are obtained by using the approach based on the differential theory of operators in a Banach space and the quadrature error estimates via Lie commutator bounds. The global error estimate is obtained via Lady Windermere's fan argument. Finally, to confirm the expected convergence order, numerical examples are studied.Article Citation - WoS: 1Corrigendum: on Density Theorems for Rings of Krull Type With Zero Divisors(TUBITAK, 2017) Ay Saylam, BaşakThis corrigendum is written to correct some parts of the paper "On density theorems for rings of Krull type with zero divisors". The proofs of Proposition 2.4 and Proposition 4.3 are incorrect and the current note makes the appropriate corrections.Article Citation - WoS: 3Citation - Scopus: 3Cloning, Expression, and Activity Analysis of Human Cathepsin C in the Yeast Pichia Pastoris(TUBITAK, 2017) Dağlıoğlu, CenkThe yeast Pichia pastoris expression system was investigated for the production of human cathepsin C (CatC) recombinant protein. The full-length CatC cDNA, corresponding to amino acids 12-475, was synthesized from interleukin-2 (IL-2) stimulated human peripheral blood mononuclear cells and subcloned in the pGEM-T cloning vector. After confirming the DNA sequence of the insert, the gene was cloned into the pPICZαA expression vector under the control of the methanol-inducible alcohol oxidase (AOX1) promoter and transformed to P. pastoris X-33 cells. The expressed protein was secreted into the culture medium through the α-factor mating signal sequence of the expression vector. Analysis of the culture supernatant revealed that the recombinant human CatC was secreted as a 58-kDa molecule, indicating that human CatC was accumulated in the culture supernatant as proform composed of the residual propart, the activation peptide, and the heavy and light chains. Extracellular recombinant proCatC was further activated by cysteine endoprotease papain in vitro and its activity was confirmed by assays using a synthetic substrate.