Demir, Ayşe Banu
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Demir, A. B.
Demir, Ayşe
Demir, Ayse Banu
Demir, Banu
Demir, Ayşe
Demir, Ayse Banu
Demir, Banu
Job Title
Email Address
banu.demir@ieu.edu.tr
Main Affiliation
09.01. Basic Medical Sciences
Status
Current Staff
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ORCID ID
Scopus Author ID
Turkish CoHE Profile ID
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WoS Researcher ID
Sustainable Development Goals
1NO POVERTY
0
Research Products
2ZERO HUNGER
0
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3GOOD HEALTH AND WELL-BEING
12
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4QUALITY EDUCATION
0
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5GENDER EQUALITY
0
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6CLEAN WATER AND SANITATION
0
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7AFFORDABLE AND CLEAN ENERGY
0
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8DECENT WORK AND ECONOMIC GROWTH
0
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9INDUSTRY, INNOVATION AND INFRASTRUCTURE
1
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10REDUCED INEQUALITIES
0
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11SUSTAINABLE CITIES AND COMMUNITIES
1
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12RESPONSIBLE CONSUMPTION AND PRODUCTION
0
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13CLIMATE ACTION
0
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14LIFE BELOW WATER
0
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15LIFE ON LAND
0
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16PEACE, JUSTICE AND STRONG INSTITUTIONS
0
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17PARTNERSHIPS FOR THE GOALS
0
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Documents
26
Citations
234
h-index
10
Documents
41
Citations
201
Scholarly Output
26
Articles
21
Views / Downloads
182/560
Supervised MSc Theses
0
Supervised PhD Theses
0
WoS Citation Count
85
Scopus Citation Count
77
Patents
0
Projects
1
WoS Citations per Publication
3.27
Scopus Citations per Publication
2.96
Open Access Source
17
Supervised Theses
0
| Journal | Count |
|---|---|
| Turkısh Journal of Bıochemıstry-Turk Bıyokımya Dergısı | 2 |
| Turkish Journal of Biochemistry-Turk Biyokimya Dergisi | 2 |
| FEBS Open Bio | 1 |
| Folıa Bıologıca | 1 |
| GORM:Gynecology Obstetrics & Reproductive Medicine | 1 |
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26 results
Scholarly Output Search Results
Now showing 1 - 10 of 26
Article Citation - WoS: 8Citation - Scopus: 4Questioning How To Define the Ultra-High Subgroup of Neuroblastoma Patients(Charles Univ Prague, First Faculty Medicine, 2021) Demir, A. B.; Aktas, S.; Altun, Z.; Ercetin, P.; Aktas, T. C.; Olgun, N.Neuroblastic tumours exhibit heterogeneity, which results in different therapeutic outcomes. Neuroblastoma is categorized into three major risk groups (low, intermediate, high risk). Recent identification of new genes raised the possibility of new biomarkers to identify sub-risk groups. In this retrospective cross-sectional study, we aimed to assess new biomarkers defining the ultra-high-risk subgroup within the high-risk group that differ in clinical situation with very bad prognosis. Twenty-five low- and 29 high-risk groups of patients were analysed for their expression of ALK, ATRX, HIF1a, HIF2a (EPAS), H2AFX, and ETV5 genes at the RNA level. Immunohistochemistry was performed to confirm the protein expression level of ALK. The risk group of patients was determined according to the International Neuroblastoma Risk Group Stratification System. Spearman correlation analysis and Mann-Whitney-U nonparametric test were used to assess the importance of expression levels among the groups. P < 0.05 was considered as significant. Sensitivity of the results was checked by ROC curve analysis. All analysed genes were found to be highly expressed in the high-risk group compared to the low-risk group, except for ETV5. When the ultra-high-risk and high-risk groups were compared, ALK was found to be highly expressed in the ultra-high-risk group. Our results show that ALK may be a candidate gene whose mRNA expression levels can distinguish the ultrahigh-risk subgroup of patients in the high-risk group of patients with non-familial neuroblastoma.Article Citation - WoS: 2Citation - Scopus: 2Analysis of Nucleotide Changes in Rt-Pcr Primer/Probe Binding Regions in Sars-Cov Isolates Reported From Turkey(Ankara Microbiology Soc, 2021-07-16) Demir, Ayse Banu; Bulgurcu, Alihan; Appak, Ozgur; Sayiner, Ayca ArzuThe SARS-CoV-2 virus, which caused the COVID-19 epidemic, caused more than 55 million cases and nearly 1.5 million deaths worldwide. For the microbiological diagnosis of the disease, the most valid method is detecting the presence of the viral genome by real-time reverse transcription polymerase chain reaction (rRT-PCR). However, due to the nature of the RNA viruses, frequent mutations may affect the sensitivity of the analyses made on the genetic material of the virus, such as PCR. In this study, we aimed to investigate the mutations in the primer-probe binding regions of the rRT-PCR panels used in COVID-19 diagnosis. SARS-CoV-2 whole genome sequence data (n= 194) isolated from COVID-19 cases in Turkey and uploaded on GISAID database from the centers in Istanbul (n= 78), Ankara (n= 58), Kars (n= 47), Bursa (n= 2), Adiyaman (n= 2), Erciyes (n= 1) and Kocaeli (n= 1) between March 17-September 14, 2020 were analyzed. In order to determine the nucleotide changes, SARS-CoV-2 sequences from Turkey were compared to the reference genome sequence (NC_045512.1) present in GenBank website. The constructed data set was aligned using the MAFFT program and was checked manually if the sequences were in the same frame by using the AliView program. Primer-probe binding sites of the thirteen SARS-CoV-2 rRT-PCR panels from seven different institutes (US CDC, China CDC, Charite CDC, Pasteur, HKU, Thailand, NIID) that are being used in COVID-19 diagnosis were evaluated in terms of nucleotide changes within the corresponding regions compared to the reference genome. Sequence diversities in the viral genomes were determined via positional nucleotide numerical calculator and entropy calculator modules and nucleotide and entropy changes in primer-probe binding regions for each rRT-PCR panel were examined. Among thirteen different primer-probe panels, nucleotide changes in the target regions of the seven primer-probe panels were determined. When viral sequences with nucleotide changes in the primer-probe binding regions were examined, the most common changes were observed in the China CDC N-forward primer and US CDC N3-forward primer binding regions. It is important that the kits to be used as diagnostic tests are designed specific to the regions with less nucleotide changes. Nucleotide changes may not be critical for DNA amplification for most PCR panels, but should be carefully monitored as they may affect the sensitivity of the assay. If the risk of alteration of the designed region is high, the primer - probe binding sites should be checked frequently and updated when necessary.Article Determination of a New Biomarker at the Level of Gene Alteration in Cisplatin Ototoxicity(MDPI, 2025-09-12) Kizmazoglu, Deniz; Erol, Aylin; Aktas, Tekincan Cagri; Olgun, Yuksel; Demir, Ayse Banu; Altun, Zekiye; Olgun, NurCisplatin is an alkylating chemotherapeutic drug used in the treatment of many pediatric solid tumors, and cisplatin ototoxicity is characterized by sensorineural, bilateral, irreversible, and progressive hearing loss. The aim of this study is to identify biomarkers that may serve as predictors of cisplatin-induced ototoxicity in pediatric cancers. In our preliminary study, patients with severe hearing loss were analyzed using the comparative genomic hybridization (CGH) method. Mutations were identified in the following genes: ADAM6, SIX3, GNAS, NDUFV1, H19, DEFA4, and ZIM2. Based on these data, we aimed to investigate the mutation status of these candidate genes in a larger population of pediatric cancer patients treated with cisplatin. DNA samples were extracted from the mononuclear cells of peripheral blood samples obtained from 82 patients. These genes were analyzed using the RT-PCR technique, and ototoxicity was assessed using the Brock and Muenster classifications. Hearing loss was detected in 28% of patients; 76.8% and 23.2% had mild and severe hearing loss, respectively. A significant correlation was found between ZIM2 gene amplification and the presence of ototoxicity (rho = 0.461, p = 0.003), especially in advanced-stage cancer patients with severe hearing loss (rho = 0.38, p = 0.017). Our findings suggest that ZIM2 is a promising biomarker for predicting cisplatin ototoxicity.Conference Object The Common Pathways Affected by Inhibition of Toll-Like Protein in Hepatocellular Carcinoma Cell Lines That May Play Role in Doxorubicin Resistance(Wiley, 2023) Demir, A. B.; Yetkin, S.; Alotaibi, H.; Atabey, N.; Koc, A.Article Citation - WoS: 1Citation - Scopus: 1Differential Effects of Choline on TLR2/4 Mediated Signaling Through Possible Regulation of Toll-Interacting Protein in Hepatocellular Carcinoma Cell Lines(Walter de Gruyter GmbH, 2024-05-30) Barış, Elif; Demir, Ayse BanuObjectives: Toll-like receptor (TLR) mediated inflammatory status plays an important role in development and pro- gression of hepatocellular carcinoma (HCC). Toll-interacting protein (TOLLIP) has an inhibitory effect on TLR-mediated inflammatory signalling and expression profile of TOLLIP varies between malignancies including HCC. Cholinergic anti-inflammatory pathway (CAP) is an endogenous mech- anism that controls inflammatory status via α7nicotinic acetylcholine receptors (α7nAChR). This study aims to investigate the effect of CAP-acting agent choline on TOLLIP and its related TLR-mediated inflammatory response in HCC cells with distinct differentiation stages. Methods: The expression patterns of α7nAChR, TLR2/4, TOLLIP, IL6, NFkB genes were evaluated by RT-PCR and ELISA in the presence of choline, along with the real-time cell proliferation and migration in HEP3B and SNU449 HCC cell lines. The interaction between choline and TOLLIP assessed by using in-silico analyses. Results: Choline downregulated TOLLIP in Hep3B and SNU449 cells. However, the expressions of α7nAChR, NF-κB, IL-6, TLR2 and TLR4 showed a decreased pattern in well differentiated HEP3B cells, while an increased pattern in poorly differentiated SNU449 cells. Conclusions: Choline might exert differential effects in TLR2/4-dependent signalling based on the differentiation stages of the HCC cells, suggesting its potential therapeutic effects in earlier stages of HCC which might be result of its partial modulation of TOLLIP.Article Citation - WoS: 1Citation - Scopus: 1The Impact of Visual Thinking in Medical Education(Walter De Gruyter Gmbh, 2021-10-23) Demir, Ayse Banu; Okuyan; van Eck, Alexander; Mura, Gokhan; Gonlugur, Emre; Karaca, Can; Abacioglu, Hakan; Okuyan, ZuhalBackground Considering medical humanities, medicine and art are two areas that resemble each other at several features. Clinical diagnosis involves the observation, description and interpretation of information of which visual ones take an important one. The skills described are important skills in the field of visual arts, as well. Underlying a good clinical practice; clinical examination and observation skills constitute an important place. Although in several studies, these skills are shown to be improved by analyzing visual art pieces, courses intended to improve visual thinking skills are not that much common in medical faculty curriculums. Materials and methods In this article, we share our opinion about the use of visual thinking in medical education by providing preliminary reflection results of learners from the second year of medical education about the visual thinking course that we have recently started to apply in Faculty of Medicine in collaboration with Faculty of Fine Arts in Izmir University of Economics in order to improve the observational skills of learners. Results Reflection results of the learners support the view that training art-viewing skill is helpful to improve observational and descriptive skills. Conclusions Increasing interdisciplinary programs on visual thinking in medical curriculums have the potential to overcome several professional development challenges in clinics.Article Citation - WoS: 17Citation - Scopus: 18Evidence for Mutations in Sars-Cov Italian Isolates Potentially Affecting Virus Transmission(Wiley, 2020-06-19) Benvenuto, Domenico; Demir, Ayse Banu; Giovanetti, Marta; Bianchi, Martina; Angeletti, Silvia; Pascarella, Stefano; Cauda, Roberto; Cassone, AntonioItaly is the first western country suffering heavy severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission and disease impact after coronavirus disease-2019 pandemia started in China. Even though the presence of mutations on spike glycoprotein and nucleocapsid in Italian isolates has been reported, the potential impact of these mutations on viral transmission has not been evaluated. We have compared SARS-CoV-2 genome sequences from Italian patients with virus sequences from Chinese patients. We focussed upon three nonsynonymous mutations of genes coding for S(one) and N (two) viral proteins present in Italian isolates and absent in Chinese ones, using various bioinformatics tools. Amino acid analysis and changes in three-dimensional protein structure suggests the mutations reduce protein stability and, particularly for S1 mutation, the enhanced torsional ability of the molecule could favor virus binding to cell receptor(s). This theoretical interpretation awaits experimental and clinical confirmation.Article Citation - WoS: 15Citation - Scopus: 17Identification of the Nucleotide Substitutions in 62 Sars-Cov Sequences From Turkey(Tubitak Scientific & Technical Research Council Turkey, 2020-06-21) Demir, Ayse Banu; Benvenuto, Domenico; Abacioglu, Hakan; Angeletti, Silvia; Ciccozzi, MassimoA previously unknown coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has been shown to cause coronavirus disease 2019 (COVID-19) pandemic. The first case of COVID-19 in Turkey has been declared in March 11th, 2020 and from there on, more than 150,000 people in the country have been diagnosed with the disease. In this study, 62 viral sequences from Turkey, which have been uploaded to GISAID database, were analyzed by means of their nucleotide substitutions in comparison to the reference SARS-CoV-2 genome from Wuhan. Our results indicate that the viral isolates from Turkey harbor some common mutations with the viral strains from Europe, Oceania, North America and Asia. When the mutations were evaluated, C3037T, C14408T and A23403G were found to be the most common nucleotide substitutions among the viral isolates in Turkey, which are mostly seen as linked mutations and are part of a haplotype observed high in Europe.Conference Object The Role of CUE5 on Protein Aggregation Under Heat Shock Stress in Saccharomyces Cerevisiae(Wiley, 2025) Kocabas, D.; Chawla, S.; Molin, M.; Demir, A. B.Article Citation - WoS: 1Citation - Scopus: 1Toll-Interacting Protein May Affect Doxorubicin Resistance in Hepatocellular Carcinoma Cell Lines(Springer, 2023-08-29) Demir, Ayşe Banu; Barış, Elif; Kaner, Umay Bengi; Alotaibi, Hani; Atabey, Nese; Koc, AhmetBackgroundLiver cancer is the third leading cause of cancer-related deaths worldwide, and hepatocellular carcinoma (HCC) is the most common type of liver cancer. Transarterial interventions are among the chemotherapeutic approaches used in hardly operable regions prior to transplantation, and in electrochemotherapy, where doxorubicin is used. However, the efficacy of treatment is affected by resistance mechanisms. Previously, we showed that overexpression of the CUE5 gene results in doxorubicin resistance in Saccharomyces cerevisiae (S. cerevisiae). In this study, the effect of Toll-interacting protein (TOLLIP), the human ortholog of CUE5, on doxorubicin resistance was evaluated in HCC cells to identify its possible role in increasing the efficacy of transarterial interventions.Methods and resultsThe NIH Gene Expression Omnibus (GEO) and Oncomine datasets were analyzed for HCC cell lines with relatively low and high TOLLIP expression, and SNU449 and Hep3B cell lines were chosen, respectively. TOLLIP expression was increased by plasmid transfection and decreased by TOLLIP-siRNA in both cell lines and evaluated by RT-PCR and ELISA. Cell proliferation and viability were examined using xCELLigence and MTT assays after doxorubicin treatment, and growth inhibitory 50 (GI 50) concentrations were evaluated. Doxorubicin GI 50 concentrations decreased approximately 2-folds in both cell lines upon silencing TOLLIP after 48 h of drug treatment.ConclusionsOur results showed for the first time that silencing TOLLIP in hepatocellular carcinoma cells may help sensitize these cells to doxorubicin and increase the efficacy of chemotherapeutic regimens where doxorubicin is used.
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