Scopus İndeksli Yayınlar Koleksiyonu / Scopus Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/11147/7148
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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: 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: 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.Article Citation - WoS: 1Citation - Scopus: 1Recursion Formula for the Green's Function of a Hamiltonian for Several Types of Dirac Delta-Function Potentials in Curved Spaces(TUBITAK, 2016) Erman, FatihIn this short article, we nonperturbatively derive a recursive formula for the Green's function associated with finitely many point Dirac delta potentials in one dimension. We extend this formula to the one for the Dirac delta potentials supported by regular curves embedded in two-dimensional manifolds and for the Dirac delta potentials supported by two-dimensional compact manifolds embedded in three-dimensional manifolds. Finally, this formulation allows us to find the recursive formula of the Green's function for the point Dirac delta potentials in two- and three-dimensional Riemannian manifolds, where the renormalization of coupling constant is required.Article It Is Sufficient To Set the Cosmological Constant To Zero or To a Small Number at an Initial Time(TUBITAK, 2016) Erdem, RecaiI point out a simple but usually overlooked fact about the cosmological constant problem: to solve the cosmological constant problem it is sufficient to find a symmetry or mechanism that sets the cosmological constant to zero or to a tiny value at some time in the past, provided that general relativity is the relevant theory of gravity, and the energy-momentum tensor (excluding the part of the form of a cosmological constant) is conserved. The relevant symmetry or mechanism need not be applicable today. Any additional cosmological constant term induced by a phase transition in the energy-momentum tensor in this case is compensated by a shift in the cosmological constant term of gravitational origin.Article Citation - WoS: 1Citation - Scopus: 3Detection of the Contamination Sources of Listeria Monocytogenes in Pickled White Cheese Production Process Line and Genotyping With the Pulsed-Field Gel Electrophoresis Method(TUBITAK, 2016) Telli, Nihat; Güner, Ahmet; Soyer Dönmez, Ferda; Özdemir, Özgün ÖyküThis study was conducted to determine the contamination sources, serotyping profiles, and antibiotic resistance patterns of Listeria monocytogenes isolated during the production of pickled white cheese. The genetic-relatedness of the isolates to EGD SLCC (5835) (1/2a, lineage II) and ATCC (13932) (4b, lineage I) reference strains was also determined with pulsed-field gel electrophoresis (PFGE) as a result of digestions with AscI and ApaI enzymes. Samples were collected from 16 different points in the production process of 4 different plants at 3 different times. Among the 192 samples examined, 17 (8.85%) were determined to be contaminated with Listeria spp. Three isolates (3.53%) obtained from raw milk, wall/ground, and press cases were identified as L. monocytogenes via the conventional culture method and confirmed by polymerase chain reaction. These isolates were found to belong to serotype 4b. According to antibiotic resistance testing against 10 antibiotics (ampicillin, gentamicin, erythromycin, tetracycline, chloramphenicol, cefalotin, streptomycin, vancomycin, penicillin, and sulfamethoxazole/trimethoprim), it was determined that isolates from raw milk and press cases were resistant to erythromycin. PPGE band patterns of the isolates displayed indistinguishable with AscI and 80%-94% homology with ApaI. The isolates were observed to display high homology to ATCC (13932) and lower homology to EGD SLCC (5835) obtained by both enzymes.
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