Browsing by Author "Kahraman E."
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Item Aurora kinase A (AURKA) and never in mitosis gene A-related kinase 6 (NEK6) genes are upregulated in erosive esophagitis and esophageal adenocarcinoma(2012) Kasap E.; Boyacioglu S.Ö.; Korkmaz M.; Yuksel E.S.; Ünsal B.; Kahraman E.; Özütemiz Ö.; Yuceyar H.Gastroesophageal reflux disease is a risk factor for esophageal adenocarcinoma yet studies that have investigated the relationship between erosive esophagitis and esophageal adenocarcinoma have usually focused on symptom-related evidence or polymorphisms. There are no epigenetic gene expression studies on this topic. In this study, we aimed to evaluate the relationship between erosive esophagitis and esophageal adenocarcinoma to identify whether there is a genetic predisposition for esophageal adenocarcinoma. The Human Epigenetic Chromatin Modification Enzyme RT 2 Profiler™ PCR array (PAHS-085A) was used to detect the expression of 84 key genes encoding enzymes. This was carried out prospectively for samples from 60 patients (20 patients as a control group, 20 patients with erosive esophagitis and 20 patients with esophageal adenocarcinoma). AURKA, AURKB, NEK6 were expressed at significantly higher levels in esophageal adenocarcinoma compared to the control group. MBD2 was expressed at significantly lower levels in the esophageal adenocarcinoma group compared to the control group. AURKA, AURKC, HDAC9 and NEK6 were expressed at significantly higher levels in erosive esophagitis compared to the control group. There was no difference in upregulated gene expression between the erosive esophagitis and esophageal adenocarcinoma. MBD2 was significantly downregulated in esophageal adenocarcinoma compared to erosive esophagitis. NEK6 and AURKA were significantly upregulated in esophageal adenocarcinoma and erosive esophagitis compared to the control group. This is a novel study on the genetic predisposition for erosive esophagitis and esophageal adenocarcinoma. AURKA and NEK6 are two promising genetic markers for erosive esophagitis and esophageal adenocarcinoma.Item GSTP1 gene methylation profiles in Helicobacter pylori (+) and (-) antral intestinal metaplasia and distal gastric tumour patients in Turkish population(2012) Asik-Sen G.; Kasap E.; Orenay-Boyacioglu S.; Korkmaz M.; Kahraman E.; Unsal B.; Yüksel-Saritas E.; Yuceyar H.Background/Aims: Gastric cancer (GC) is the second most common malignancy worldwide, with a high mortality rate. The incidence of GC has declined in the western countries during the last decades. The glutathione S-transferases comprise a group of enzymes that are critical in the detoxification of carcinogens. In this study we aimed at the relationship GSTP-1 methylation in patients with intestinal metaplasia with and without Helicobacter pylori infection, gastric cancer and controls. Methodology: The methylation status of GSTP1 gene was analyzed by methylation specific PCR after bisulfate modification in H. pylori (+) (n=25) and (-) (n=25) intestinal metaplasia (IM) patients, GC (n=25) and control subjects (n=15) between September 2009 to November 2011. Results: During the study period 90 patients who underwent endoscopic examination were included in the study. When we considered the GSTP1 gene methylation profile in all of the groups; 26 (28%) patients had methylated GSTP1 gene, 31 (34%) patients had unmethylated GSTP1 gene and 33 (36%) patients had heterogeneously methylated GSTP1 gene. Conclusions: GSTP1 gene methylation profile is not appropriate for early diagnosis of cases with gastric cancer. © H.G.E. Update Medical Publishing S.A.Item Biological effects of tolerable level chronic boron intake on transcription factors(Elsevier GmbH, 2017) Orenay Boyacioglu S.; Korkmaz M.; Kahraman E.; Yildirim H.; Bora S.; Ataman O.Y.The mechanism of boron effect on human transcription and translation has not been fully understood. In the current study it was aimed to reveal the role of boron on the expression of certain transcription factors that play key roles in many cellular pathways on human subjects chronically exposed to low amounts of boron. The boron concentrations in drinking water samples were 1.57 ± 0.06 mg/l for boron group while the corresponding value for the control group was 0.016 ± 0.002 mg/l. RNA isolation was performed using PAX gene RNA kit on the blood samples from the subjects. The RNA was then reverse transcribed into cDNA and analyzed using the Human Transcription Factors RT2 Profiler™ PCR Arrays. While the boron amount in urine was detected as 3.56 ± 1.47 mg/day in the boron group, it was 0.72 ± 0.30 mg/day in the control group. Daily boron intake of the boron and control groups were calculated to be 6.98 ± 3.39 and 1.18 ± 0.41 mg/day, respectively. The expression levels of the transcription factor genes were compared between the boron and control groups and no statistically significant difference was detected (P > 0.05). The data suggest that boron intake at 6.98 ± 3.39 mg/day, which is the dose at which beneficial effects might be seen, does not result in toxicity at molecular level since the expression levels of transcription factors are not changed. Although boron intake over this level will seem to increase RNA synthesis, further examination of the topic is needed using new molecular epidemiological data. © 2016 Elsevier GmbHItem THE SOLUTION OF THE GOVERNING EQUATION OF THE BEAM ON LINEAR SPRING FOUNDATION MODELED BY A DISCONTINUITY FUNCTION(Yildiz Technical University, 2019) DÖNMEZ Demır D.; Sinir B.G.; Kahraman E.The structural engineering researches have attracted considerable attention by many scientist for several decades. Determining the dynamical behaviors of structural elements with some discontinuous is of great importance in many engineering applications. The mentioned structures can be modelled two different ways. In the first approximation so-called the classical approach, a fourth order differential equation are written for each part of beam separated in the distinct discontinuity locations. Therefore, we obtain a system of equation containing n + 1 number of the differential equation with boundary and transient conditions. Secondly, the real problem can be reformulated by only one differential equation having discontinuity function. In this study, we introduce the method of multiple scales as the solution technique. Since we encountered by the differential equation with discontinuity function in the part of order discretization during the perturbative solution, we have used a numerical technique for the solution. The mentioned technique is applied on the beam model lying on lineer spring foundation called as Winkler type foundation. © 2019 Yildiz Technical University. All Rights Reserved.Item Dynamical analysis of the general beam model with singularity function(University of Kuwait, 2021) Dönmez Demir D.; Sinir B.G.; Kahraman E.The aim of this study is to present a general model with variable coefficients corresponding to some structural elements such as beam, string, bar, and rod. To solve general model with variable coefficients, a different solution procedure combining a method of multiple scales (MMS) and a finite difference method (FDM) is presented in this study. This technique provides an advantage in the numerical solution of the structural element model containing any discontinuity and in its dynamical analysis by perturbation method. Furthermore, two problems including discontinuity are considered to show the accuracy of the method presented. The comparisons of the numerical results obtained from the proposed method and classical method are introduced. © 2021 University of Kuwait. All rights reserved.