PubMed İndeksli Yayınlar Koleksiyonu / PubMed Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/11147/7645
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Article Citation - Scopus: 27Apoptotic Effects of Resveratrol, a Grape Polyphenol, Onimatinib-Sensitive and Resistant K562 Chronic Myeloid Leukemia Cells(2012) Can,G.; Cakir,Z.; Kartal,M.; Gunduz,U.; Baran,Y.Aim: To examine the antiproliferative and apoptotic effects of resveratrol on imatinib-sensitive and imatinib-resistant K562 chronic myeloid leukemia cells. Materials and Methods: Antiproliferative effects of resveratrol were determined by the 3-Bis[2-methoxy-4-nitro-5-sulphophenyl]-2H-tetrazolium-5- carboxanilide inner salt (XTT) cell proliferation assay. Apoptotic effects of resveratrol on sensitive K562 and resistant K562/IMA-3 cells were determined through changes in caspase-3 activity, loss of mitochondrial membrane potential (MMP), and apoptosis by annexin V-(FITC). Results: The concentrations of resveratrol that inhibited cell growth by 50% ( IC50) were calculated as 85 and 122 μM for K562 and K562/IMA-3 cells, respectively. There were 1.91-, 7.42- and 14.73-fold increases in loss of MMP in K562 cells treated with 10, 50, and 100 μM resveratrol, respectively. The same concentrations of resveratrol resulted in 2.21-, 3.30- and 7.65-fold increases in loss of MMP in K562/IMA-3 cells. Caspase-3 activity increased 1.04-, 2.77- and 4.8-fold in K562 and 1.02-, 1.41- and 3.46-fold in K562/IMA- 3 cells in response to the same concentrations of resveratrol, respectively. Apoptosis was induced in 58.7%-and 43.3% of K562 and K562/IMA-3 cells, respectively, in response to 100 μM resveratrol. Conclusion: Taken together these results may suggest potential use of resveratrol in CML, as well as in patients with primary and/or acquired resistance to imatinib.Article Citation - WoS: 37Mechanisms of Cellular Resistance To Imatinib in Human Chronic Myeloid Leukemia Cells(Taylor and Francis Ltd., 2007) Baran, Yusuf; Ural, Ali Uğur; Gündüz, UfukA major advancement in the treatment of chronic myeloid leukemia (CML) has been the development of imatinib, which has shown striking activity in the chronic phase and the accelerated phase, but less so in the blast phase of the disease. Despite high rates of hematologic and cytogenetic responses to therapy, the emergence of resistance to imatinib has been recognized as a major problem in the treatment of patients with CML. Various cellular mechanisms may be involved in the nature of cellular resistance. Increased amount of target, alteration in structure of target proteins, decreased drug uptake and increased detoxification are well-known mechanisms of resistance. On the other hand, in some cases, even if anticancer drugs reach their sites of action, bypassing drug efflux system of the cells, some cells still may survive via the dysregulation of apoptotic signalling. In this study, mechanisms of resistance to imatinib-induced apoptosis in human Meg-01 CML cells were examined. Continuous exposure of cells to step-wise increasing concentrations of imatinib resulted in the selection of 200- and 1000 nM imatinib-resistant sub-lines referred to as Meg-01/IMA-0,2 and Meg-01/1MA-1, respectively. MTT cell proliferation, cell cycle analyses and trypan blue dye exclusion analyses showed that Meg-0l/IMA-1 cells were resistant to imatinib-induced apoptosis as compared to parental sensitive cells. There was an increased expression of BCR/ABL, Bcl-2 and an increase in mitochondrial membrane potential (MMP) detected in resistant cells comparing to parental sensitive cells. There was no mutation detected in imatinib binding site of ABL kinase region. Various diverse mechanisms have been reported for their involvement in the multidrug resistance. In this study, it has been shown that the degree of BCR/ABL expression appears to be directly proportional to the levels of imatinib resistance. In addition, there have been BCR/ABL-independent mechanisms reported for deriving resistance against imatinib. Our results revealed that besides BCR/ABL overexpression, imatinib resistance also depends on the inhibition of apoptosis as a result of up-regulation of anti-apoptotic stimuli and down-regulation of pro-apoptotic stimuli through MMP but does not depend on any mutation on imatinib binding site of ABL kinase.Article Citation - WoS: 12Citation - Scopus: 14Prevalence, Virulence Characterization, and Genetic Relatedness of Listeria Monocytogenes Isolated From Chicken Retail Points and Poultry Slaughterhouses in Turkey(Springer, 2019) Çoban, Ayşen; Pennone, Vincenzo; Sudağıdan, Mert; Molva, Çelenk; Jordan, Kieran; Aydın, AliListeria monocytogenes is one of the most important foodborne pathogens and is a causal agent of listeriosis in humans and animals. The aim of this study was to determine the prevalence, serogroups, antibiotic susceptibility, virulence factor genes, and genetic relatedness of L. monocytogenes strains isolated from 500 poultry samples in Turkey. The isolation sources of 103 L. monocytogenes strains were retail markets (n = 100) and slaughterhouses (n = 3). L. monocytogenes strains were identified as serogroups 1/2a-3a (75.7%, lineage I), 1/2c-3c (14.56%, lineage I), 1/2b-3b-7 (5.82%, lineage II), 4a-4c (2.91%, lineage III), and 4b-4d-4e (0.97%, lineage III). Most of the L. monocytogenes strains (93.2%) were susceptible to the antibiotics tested. PCR analysis indicated that the majority of the strains (95% to 100%) contained most of the virulence genes (hylA, plcA, plcB, prfA, mpl, actA, dltA, fri, flaA inlA, inlC, and inlJ). Pulsed-field gel electrophoresis (PFGE) demonstrated that there were 18 pulsotypes grouped at a similarity of >90% among the strains. These results indicate that it is necessary to prevent the presence of L. monocytogenes in the poultry-processing environments to help prevent outbreaks of listeriosis and protect public health.Editorial Citation - WoS: 8Citation - Scopus: 9Kras(g12c) Inhibitors on the Horizon(Future Science, 2019) Çağır, Ali; Azmi, Asfar S.RAS proteins (the four isoforms KRAS4A, KRAS4B, NRAS and HRAS encoded by three genes KRAS, NRAS and HRAS) act as molecular switches that when activated drive several key cellular processes such as cell growth, proliferation and survival [1]. In normal cells, RAS activity is under tight control by the precise activation (binding to GTP) and inactivation (GTP hydrolysis to GDP) [1]. As with other critical proteins, it is not at all surprising to note that the gene encoding the RAS protein isoforms is found mutated or altered in a significant proportion of tumors [2]. Mutant RAS loses its ability to hydrolyze GTP and remains in a permanently activated state (bound to GTP) leading to uncontrolled growth.Article Citation - WoS: 5Modeling Growth of Alicyclobacillus Acidoterrestris Dsm 3922 Type Strain Vegetative Cells in the Apple Juice With Nisin and Lysozyme(AIMS Press, 2017) Molva, Çelenk; Baysal, Ayşe HandanIn the present study, the effect of storage temperature on A. acidoterrestris DSM 3922 cells (105 CFU/mL) was examined during growth in reconstituted apple juice (pH 3.8, degrees Brix 11.3) containing nisin (0-100 IU/mL) and lysozyme (0-100 mg/L). The growth curves were obtained at three temperatures of 27, 35 and 43 degrees C using absorbance data (OD600nm). Based on the results, the minimal inhibitory concentrations (MICs) of nisin were found as 10 IU/mL at all tested temperatures. On the other hand, increasing the temperature decreased the amount of lysozyme for growth inhibition. The MICs of lysozyme were found as 10, 2.5 and 1.25 mg/L at 27, 35 and 43 degrees C, respectively. At selected non-inhibitory doses, nisin (1.25-5 IU/mL) and lysozyme (0.3-2.5 mg/L) prolonged the lag time compared to the controls at the corresponding temperatures. In addition, there was a strong linear relationship between the lag time and lysozyme concentrations at 27 and 35 degrees C (R-2 > 0.98). The results of this study demonstrated that both nisin and lysozyme could be used to inhibit the growth of A. acidoterrestris cells in the apple juice. The results also indicated that the growth parameters were variable depending on the storage temperature and the type of the antimicrobial agent used in the apple juice.Article Citation - WoS: 3Citation - Scopus: 5A Novel Thermophilic Hemoprotein Scaffold for Rational Design of Biocatalysts(Springer Verlag, 2018) Efua Aggrey Fynn, Joana; Sürmeli, Nur BaşakHemoproteins are commonly found in nature, and involved in many important cellular processes such as oxygen transport, electron transfer, and catalysis. Rational design of hemoproteins can not only inspire novel biocatalysts but will also lead to a better understanding of structure-function relationships in native hemoproteins. Here, the heme nitric oxide/oxygen-binding protein from Caldanaerobacter subterraneus subsp. tengcongensis (TtH-NOX) is used as a novel scaffold for oxidation biocatalyst design. We show that signaling protein TtH-NOX can be reengineered to catalyze H2O2 decomposition and oxidation of 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulphonic acid) by H2O2. In addition, the role of the distal tyrosine (Tyr140) in catalysis is investigated. The mutation of Tyr140 to alanine hinders the catalysis of the oxidation reactions. On the other hand, the mutation of Tyr140 to histidine, which is commonly observed in peroxidases, leads to a significant increase of the catalytic activity. Taken together, these results show that, while the distal histidine plays an important role in hemoprotein reactions with H2O2, it is not always essential for oxidation activity. We show that TtH-NOX protein can be used as an alternative scaffold for the design of novel biocatalysts with desired reactivity or functionality. H-NOX proteins are homologous to the nitric oxide sensor soluble guanylate cyclase. Here, we show that the gas sensor protein TtH-NOX shows limited capacity for catalysis of redox reactions and it can be used as a novel scaffold in biocatalysis design. [GRAPHICS] .Article Citation - WoS: 10Citation - Scopus: 10The Effect of Additional Telerounding on Postoperative Outcomes, Patient and Surgeon Satisfaction Rates in the Patients Who Underwent Percutaneous Nephrolithotomy(Iniestares, S.A., 2019) Aydoğdu, Özgü; Şen, Volkan; Yarımoğlu, Serkan; Aydoğdu, Canan; Bozkurt, İbrahim H.; Yonguç, TarıkINTRODUCTION: We wanted to investigate the potential effect of additional telerounding system on postoperative outcomes, patient and surgeon satisfaction rates in the patients who underwent percutaneous nephrolithotomy (PNL). METHODS: Eighty patients who underwent PNL were included in the study. The patients were randomly divided to two groups. Group 1 included 40 patients who were followed-up with standard rounds and group 2 included 40 patients who were followed-up with telerounding in addition to standard rounds. Patient and surgeon satisfaction rates were assessed with a visual analog scale (VAS) where 0 point represents very dissatisfied and 100 points very satisfied. RESULTS: Mean time of preoperative telerounding visit was 3.65 +/- 0.59 (2-4) minutes. Mean time of telerounding visits on the postoperative 1st and 2nd days was 3.80 +/- 0.62 and 2.9 +/- 0.91 minutes respectively. The VAS score evaluating the surgeon's satisfaction rate for telerounding was 91 +/- 11.2 and patients expressed a high level of satisfaction with 72.5%. CONCLUSION: The use of additional telerounding in urological patient care provides high satisfaction rates for both the patients and the surgeon. However the findings of the present study don't underestimate the importance of personal surgeon-patient interaction.Article Citation - WoS: 14Citation - Scopus: 18Separating Normosmic and Anosmic Patients Based on Entropy Evaluation of Olfactory Event-Related Potentials(Elsevier Ltd., 2019) Güdücü, Çağdaş; Olcay, Bilal Orkan; Schaefer, L.; Aziz, M.; Schriever, V. A.; Özgören, Murat; Hummel, T.Objective: Methods based on electroencephalography (EEG) are used to evaluate brain responses to odors which is challenging due to the relatively low signal-to-noise ratio. This is especially difficult in patients with olfactory loss. In the present study, we aim to establish a method to separate functionally anosmic and normosmic individuals by means of recordings of olfactory event-related potentials (OERP) using an automated tool. Therefore, Shannon entropy was adopted to examine the complexity of the averaged electrophysiological responses. Methods: A total of 102 participants received 60 rose-like odorous stimuli at an inter-stimulus interval of 10 s. Olfactory-related brain activity was investigated within three time-windows of equal length; pre-, during-, and post-stimulus. Results: Based on entropy analysis, patients were correctly diagnosed for anosmia with a 75% success rate. Conclusion: This novel approach can be expected to help clinicians to identify patients with anosmia or patients with early symptoms of neurodegenerative disorders. Significance: There is no automated diagnostic tool for anosmic and normosmic patients using OERP. However, detectability of OERP in patients with functional anosmia has been reported to be in the range of 50%.Article Citation - WoS: 10Citation - Scopus: 13Analysis of European Hazelnut (corylus Avellana) Reveals Loci for Cultivar Improvement and the Effects of Domestication and Selection on Nut and Kernel Traits(Springer Verlag, 2019) Frary, Amy; Öztürk, Süleyman Can; Balık, Hüseyin İrfan; Kayalak Balık, Selda; Kızılcı, Gökhan; Doğanlar, Sami; Frary, AnneTurkey is a rich source of European hazelnut (Corylus avellana) germplasm with nearly 400 accessions in the national collection. This genetic material encompasses cultivars, landraces and wild genotypes which were characterized for 12 nut and 13 kernel traits over 2years in the 1990s. Analysis of these attributes revealed both the positive and negative impacts that human selection and breeding have had on hazelnut. Thus, while selection has resulted in larger nuts and kernels, cultivars have fewer nuts per cluster and kernels with larger internal cavities. Breeding has also resulted in a propensity for cultivars to have higher proportions of double kernels and empty nuts, two traits which reduce quality and yield. In addition, it is clear that while selection has successfully increased hazelnut fat content it has not impacted overall flavor, a much more complex trait. The nut and kernel phenotypic data were combined with genotypic data from 406 simple sequence repeat marker alleles for association mapping of the quantitative trait loci (QTL) for the traits. A total of 78 loci were detected in the population with the highest proportions for nut (24%) and kernel (26%) appearance parameters followed by quality (19%), shell thickness (16%) and yield-related (15%) traits. It is hoped that some of the identified QTL will be useful for future breeding of hazelnut for improved nut and kernel yield and quality.Article Citation - WoS: 3Citation - Scopus: 3Monolayer Aste2: Stable Robust Metal in 2d, 1d and 0d(Wiley, 2018) Badalov, S. V.; Kandemir, Ali; Şahin, HasanThe structural, phononic, and electronic properties of the monolayer structures of AsTe2 are characterized by performing density functional theory (DFT) calculations. Total energy optimization and phonon calculations reveal that single layers of the 2H-AsTe2 and 1T-AsTe2 phases form dynamically stable crystal structures. Electronic structure analysis also shows that both 2H and 1T phases have nonmagnetic metallic character. It is also predicted that the metallic nature of the ultra-thin both 2H-AsTe2 and 1T-AsTe2 structures remain unchanged even under high biaxial strain values. For further examination of the dimensionality effect in the robust metallicity in 2D AsTe2 phases, electronic characteristics of 1D nanoribbons and 0D quantum dots are also investigated. It is found that independent from the dimension and crystallographic orientations 0D and 1D structures of 2H- and 1T-AsTe2 structures have metallic behavior. It is found that single layers of AsTe2 are quite promising materials for nanodevice applications owing to the robust metallic character.