PubMed İndeksli Yayınlar Koleksiyonu / PubMed Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/11147/7645
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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: 13Citation - Scopus: 13Cycloartane-Type Sapogenol Derivatives Inhibit Nf?b Activation as Chemopreventive Strategy for Inflammation-Induced Prostate Carcinogenesis(Elsevier Ltd., 2018) Debeleç Bütüner, Bilge; Öztürk, Mert Burak; Tağ, Özgür; Akgün, İsmail Hakkı; Yetik Anacak, Günay; Bedir, Erdal; Korkmaz, Kemal SamiChronic inflammation is associated to 25% of cancer cases according to epidemiological data. Therefore, inhibition of inflammation-induced carcinogenesis can be an efficient therapeutic approach for cancer chemoprevention in drug development studies. It is also determined that anti-inflammatory drugs reduce cancer incidence. Cell culture-based in vitro screening methods are used as a fast and efficient method to investigate the biological activities of the biomolecules. In addition, saponins are molecules that are isolated from natural sources and are known to have potential for tumor inhibition. Studies on the preparation of analogues of cycloartane-type sapogenols (9,19-cyclolanostanes) have so far been limited. Therefore we have decided to direct our efforts toward the exploration of new anti-tumor agents prepared from cycloastragenol and its production artifact astragenol. The semi-synthetic derivatives were prepared mainly by oxidation, condensation, alkylation, acylation, and elimination reactions. After preliminary studies, five sapogenol analogues, two of which were new compounds (2 and 3), were selected and screened for their inhibitory activity on cell viability and NFκB signaling pathway activity in LNCaP prostate cancer cells. We found that the astragenol derivatives 1 and 2 as well as cycloastragenol derivatives 3, 4, and 5 exhibited strong inhibitory activity on NFκB signaling leading the repression of NFκB transcriptional activation and suppressed cell proliferation. The results suggested that these molecules might have significant potential for chemoprevention of prostate carcinogenesis induced by inflammatory NFκB signaling pathway.Article Citation - WoS: 8Citation - Scopus: 7Secreted Wnt Antagonists in Leukemia: a Road Yet To Be Paved(Elsevier Ltd., 2018) Pehlivan, Melek; Çalışkan, Ceyda; Yüce, Zeynep; Sercan, Hakkı OgünWnt signaling has been a topic of research for many years for its diverse and fundamental functions in physiological (such as embryogenesis, organogenesis, proliferation, tissue repair and cellular differentiation) and pathological (carcinogenesis, congenital/genetic diseases, and tissue degeneration) processes. Wnt signaling pathway aberrations are associated with both solid tumors and hematological malignancies. Unregulated Wnt signaling observed in malignancies may be due to a wide spectrum of abnormalities, from mutations in the genes of key players to epigenetic modifications of Wnt antagonists. Of these, Wnt antagonists are gaining significant attention for their potential of being targets for treatment and inhibition of Wnt signaling. In this review, we discuss and summarize the significance of Wnt signaling antagonists in the pathogenesis and treatment of hematological malignancies.Article Citation - WoS: 11Citation - Scopus: 11Secondary Metabolites From Astragalus Karjaginii Boriss and the Evaluation of Their Effects on Cytokine Release and Hemolysis(Elsevier Ltd., 2017) Aslanipour, Behnaz; Gülcemal, Derya; Nalbantsoy, Ayşe; Yusufoğlu, Hasan; Bedir, ErdalA new cycloartane sapogenol and a new cycloartane xyloside were isolated from Astragalus karjaginii BORISS along with thirteen known compounds. The structures of the new compounds were established as 3-oxo-6α,16β,24(S),25-tetrahydroxycycloartane (1) and 6-O-β-D-xylopyranosyl-3β,6α,16β,24(S),25-pentahydroxycycloartane (2) by 1D- and 2D-NMR experiments as well as ESIMS and HRMS analyses. The presence of the keto function at position 3 was reported for the first time for cyclocanthogenol sapogenin of Astragalus genus. In vitro immunomodulatory effects of the new compounds (1 and 2) along with the n-BuOH and MeOH extracts of A. karjaginii at two different doses (3 and 6 μg) were tested on human whole blood for in vitro cytokine release (IL-2, IL-17A and IFN-γ) and hemolytic activities. The results confirmed that compound 2, a monodesmosidic saponin, had the strongest effect on the induction of both IL-2 (6 μg, 6345.41 ± 0.12 pg/mL (× 5), P < 0.001) and a slight effect upon IL-17A (3 μg, 5217.85 ± 0.72 pg/mL, P < 0.05) cytokines compared to the other test compounds and positive controls (AST VII: Astragaloside VII; and QS-21: Quillaja saponin 21). All tested extracts and molecules also induced release of IFN-γ remarkably ranging between 5031.95 ± 0.05 pg/mL, P < 0.001 for MeOH extract (6 μg) and 5877.08 ± 0.06 pg/mL, P < 0.001 for compound 1 (6 μg) compared to QS-21 (6 μg, 5924.87 ± 0.1 pg/mL, P < 0.001). Administration of AST VII and other test compounds did not cause any hemolytic activity, whereas QS-21 resulted a noteworthy hemolysis.Article Citation - WoS: 2Citation - Scopus: 2Observation of the Side Chain O-Methylation of Glutamic Acid or Aspartic Acid Containing Model Peptides by Electrospray Ionization-Mass Spectrometry(Elsevier Ltd., 2017) Atik, Ahmet Emin; Güray, Melda Zeynep; Yalçın, TalatO-methylation of the side chains of glutamic acid (E) and aspartic acid (D) residues is generally observed modification when an acidified methanol/water (MeOH/dH2O) mixture is used as a solvent system during sample preparation for proteomic research. This chemical modification may result misidentification with endogenous protein methylation; therefore, a special care should be taken during sample handling prior to mass spectrometric analysis. In the current study, we systematically examined the extent of E/D methylation and C-terminus carboxyl group of synthetic model peptides in terms of different incubation temperatures, storage times, and added acid types as well as its percentages. To monitor these effects, C-terminus amidated and free acid forms of synthetic model peptides comprised of E or D residue(s) have been analyzed by electrospray ionization-mass spectrometry (ESI-MS). Additionally, LC–MS/MS experiments were performed to confirm the formation of methylated peptide product. The results showed that the rate of methylation was increased as the temperature increases along with prolong incubation times. Moreover, the extent of methylation was remarkably high when formic acid (FA) used as a protonation agent instead of acetic acid (AA). In addition, it was found that the degree of methylation was significantly decreased by lowering acid percentages in ESI solution. More than one acidic residue containing model peptides have been also used to explore the extent of multiple methylation reaction. Lastly, the ethanol (EtOH) and isopropanol (iPrOH) have been substituted separately with MeOH in sample preparation step to investigate the extent of esterification reaction under the same experimental conditions. However, in the positive perspective of view, this method can be used as a simple, rapid and cheap method for methylation of acidic residues under normal laboratory conditions.Article Citation - WoS: 14Citation - Scopus: 15Neuraminidase-1 Contributes Significantly To the Degradation of Neuronal B-Series Gangliosides but Not To the Bypass of the Catabolic Block in Tay-Sachs Mouse Models(Elsevier Ltd., 2015) Timur, Zehra Kevser; Akyıldız Demir, Seçil; Marsching, C.; Sandhoff, R.; Seyrantepe, VolkanTaySachs disease is a severe lysosomal storage disorder caused bymutations in the HEXA gene coding for? subunit of lysosomal β-Hexosaminidase A enzyme, which converts GM2 to GM3 ganglioside. HexA mice, depleted of the β-Hexosaminidase A iso-enzyme, remain asymptomatic up to 1 year of age because of a metabolic bypass by neuraminidase(s). These enzymes remove a sialic acid residue converting GM2 to GA2,which is further degraded by the still intact β-Hexosaminidase B iso-enzyme into lactosylceramide. A previously identified ganglioside metabolizing neuraminidase, Neu4, is abundantly expressed in the mouse brain and has activity against gangliosides like GM2 in vitro. Neu4 mice showed increased GD1a and decreased GM1 ganglioside in the brain suggesting the importance of the Neu4 in ganglioside catabolism. Mice with targeted disruption of both HexA and Neu4 genes showed accumulating GM2 ganglioside and epileptic seizures with 40% penetrance, indicating that the neuraminidase Neu4 is a modulatory gene, but may not be the only neuraminidase contributing to the metabolic bypass in HexA mice. Therefore, we elucidated the biological role of neuraminidase-1 in ganglioside degradation in mouse. Analysis of HexANeu1 and HexANeu4Neu1 mice models showed significant contribution of neuraminidase-1 on B-series ganglioside degradation in the brain. Therefore, we speculate that other neuraminidase/neuraminidases such as Neu2 and/or Neu3 might be also involved in the ganglioside degradation pathway in HexA mice.Article Citation - WoS: 11Citation - Scopus: 9Quantification of Staphylococcus Aureus in White Cheese by the Improved Dna Extraction Strategy Combined With Taqman and Lna Probe-Based Qpcr(Elsevier Ltd., 2014) Kadiroğlu, Pınar; Korel, Figen; Ceylan, ÇağatayFour different bacterial DNA extraction strategies and two different qPCR probe chemistries were studied for detection of Stapylococcus aureus from white cheeses. Method employing trypsin treatment followed by a commercial kit application and TaqMan probe-based qPCR was the most sensitive one detecting higher counts than standards in naturally contaminated samples.Article Citation - WoS: 5Citation - Scopus: 5Targeting Foxm1 Transcription Factor in T-Cell Acute Lymphoblastic Leukemia Cell Line(Elsevier Ltd., 2015) Tüfekçi, Özlem; Kartal Yandım, Melis; Ören, Hale; İrken, Gülersu; Baran, YusufThe Forkhead box protein M1 (FoxM1) is an important transcription factor having significant roles in various cellular events. FoxM1 overexpression has been reported to be related with many types of cancer. However, it is not known whether it contributes to oncogenesis of acute lymphoblastic leukemia. Siomycin A, a thiazol antibiotic, is known to inhibit FoxM1 transcriptional activity. In this study, we aimed to determine gene expression levels of FoxM1 in Jurkat cells (T-cell acute lymphoblastic leukemia cell line) and therapeutic potential of targeting FoxM1 by siomycin A alone and in combination with dexamethasone which improves the survival of children with T-cell acute lymphoblastic leukemia (ALL). We also examined the molecular mechanisms of siomycin A and dexamethasone-induced cell death in Jurkat cells. We demonstrated that FoxM1 mRNA is highly expressed in Jurkat cells. Dexamethasone and siomycin A caused a significant reduction in gene expression levels of FoxM1 in Jurkat cells. Targeting FoxM1 by siomycin A and dexamethasone caused a significant decrease in T-ALL cell line proliferation through induction of G1 cell cycle arrest. All these findings suggest a possible role of FoxM1 in T-cell ALL pathogenesis and represent FoxM1 as an attractive target for T-cell ALL therapy. © 2014 Elsevier Ltd.Article Citation - WoS: 16Citation - Scopus: 20Automated Labelling of Cancer Textures in Colorectal Histopathology Slides Using Quasi-Supervised Learning(Elsevier Ltd., 2013) Önder, Devrim; Sarıoğlu, Sülen; Karaçalı, BilgeQuasi-supervised learning is a statistical learning algorithm that contrasts two datasets by computing estimate for the posterior probability of each sample in either dataset. This method has not been applied to histopathological images before. The purpose of this study is to evaluate the performance of the method to identify colorectal tissues with or without adenocarcinoma. Light microscopic digital images from histopathological sections were obtained from 30 colorectal radical surgery materials including adenocarcinoma and non-neoplastic regions. The texture features were extracted by using local histograms and co-occurrence matrices. The quasi-supervised learning algorithm operates on two datasets, one containing samples of normal tissues labelled only indirectly, and the other containing an unlabeled collection of samples of both normal and cancer tissues. As such, the algorithm eliminates the need for manually labelled samples of normal and cancer tissues for conventional supervised learning and significantly reduces the expert intervention. Several texture feature vector datasets corresponding to different extraction parameters were tested within the proposed framework. The Independent Component Analysis dimensionality reduction approach was also identified as the one improving the labelling performance evaluated in this series. In this series, the proposed method was applied to the dataset of 22,080 vectors with reduced dimensionality 119 from 132. Regions containing cancer tissue could be identified accurately having false and true positive rates up to 19% and 88% respectively without using manually labelled ground-truth datasets in a quasi-supervised strategy. The resulting labelling performances were compared to that of a conventional powerful supervised classifier using manually labelled ground-truth data. The supervised classifier results were calculated as 3.5% and 95% for the same case. The results in this series in comparison with the benchmark classifier, suggest that quasi-supervised image texture labelling may be a useful method in the analysis and classification of pathological slides but further study is required to improve the results.Article Citation - WoS: 34Citation - Scopus: 41Autologous Rabbit Adipose Tissue-Derived Mesenchymal Stromal Cells for the Treatment of Bone Injuries With Distraction Osteogenesis(Elsevier Ltd., 2013) Sunay, Özgür; Can, Geylani; Çakır, Zeynep; Denek, Ziya; Kozanoglu, İlknur; Erbil, Güven; Yılmaz, Mustafa; Baran, YusufBackground aims: Adipose tissue-derived mesenchymal stromal cells (MSCs) have a higher capacity for proliferation and differentiation compared with other cell lineages. Although distraction osteogenesis is the most important therapy for treating bone defects, this treatment is restricted in many situations. The aim of this study was to examine the therapeutic potential of adipose tissue-derived MSCs and osteoblasts differentiated from adipose tissue-derived MSCs in the treatment of bone defects. Methods: Bone defects were produced in the tibias of New Zealand rabbits that had previously undergone adipose tissue extraction. Tibial osteotomy was performed, and a distractor was placed on the right leg of the rabbits. The rabbits were placed in control (group I), stem cell (group II) and osteoblast-differentiated stem cell (group III) treatment groups. The rabbits were sacrificed, and the defect area was evaluated by radiologic, biomechanical and histopathologic tests to examine the therapeutic effects of adipose tissue-derived MSCs. Results: Radiologic analyses revealed that callus density and the ossification rate increased in group III compared with group I and group II. In biomechanical tests, the highest ossification rate was observed in group III. Histopathologic studies showed that the quality of newly formed bone and the number of cells active in bone formation were significantly higher in group III rabbits compared with group I and group II rabbits. Conclusions: These data reveal that osteoblasts differentiated from adipose tissue-derived MSCs shorten the consolidation period of distraction osteogenesis. Stem cells could be used as an effective treatment for bone defects.