Demir, Ayşe Banu
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Demir, A. B.
Demir, Ayşe
Demir, Ayse Banu
Demir, Banu
Demir, Ayşe
Demir, Ayse Banu
Demir, Banu
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Email Address
banu.demir@ieu.edu.tr
Main Affiliation
09.01. Basic Medical Sciences
Status
Current Staff
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Scopus Author ID
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WoS Researcher ID
Sustainable Development Goals
8
DECENT WORK AND ECONOMIC GROWTH
0
Research Products
9
INDUSTRY, INNOVATION AND INFRASTRUCTURE
1
Research Products
10
REDUCED INEQUALITIES
0
Research Products
17
PARTNERSHIPS FOR THE GOALS
0
Research Products
12
RESPONSIBLE CONSUMPTION AND PRODUCTION
0
Research Products
7
AFFORDABLE AND CLEAN ENERGY
0
Research Products
1
NO POVERTY
0
Research Products
5
GENDER EQUALITY
0
Research Products
13
CLIMATE ACTION
0
Research Products
4
QUALITY EDUCATION
0
Research Products
14
LIFE BELOW WATER
0
Research Products
2
ZERO HUNGER
0
Research Products
15
LIFE ON LAND
0
Research Products
16
PEACE, JUSTICE AND STRONG INSTITUTIONS
0
Research Products
6
CLEAN WATER AND SANITATION
0
Research Products
3
GOOD HEALTH AND WELL-BEING
8
Research Products
11
SUSTAINABLE CITIES AND COMMUNITIES
1
Research Products
Documents
26
Citations
234
h-index
10
Documents
41
Citations
201
Scholarly Output
25
Articles
20
Views / Downloads
63/319
Supervised MSc Theses
0
Supervised PhD Theses
0
WoS Citation Count
85
Scopus Citation Count
77
WoS h-index
6
Scopus h-index
4
Patents
0
Projects
1
WoS Citations per Publication
3.40
Scopus Citations per Publication
3.08
Open Access Source
16
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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25 results
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Now showing 1 - 10 of 25
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) 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) 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.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.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: 1The Impact of Visual Thinking in Medical Education(Walter De Gruyter Gmbh, 2022) Demir, Ayse Banu; Okuyan; van Eck, Alexander; Mura, Gokhan; Gonlugur, Emre; Karaca, Can; Abacioglu, HakanBackground 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: 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) 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: 6Prenatal Detection of Peters Plus-Like Syndrome(Galenos Yayincilik, 2018) Canda, Mehmet Tunc; Caglayan, Latife Doganay; Demir, Ayse Banu; Demir, NamikPeters plus syndrome is a rare congenital disorder that includes ocular anterior segment defects of the classic Peter's anomaly, and is mostly associated with craniofacial and skeletal defects. A 21-week fetus was referred for further evaluation due to a suspicion of fetal hydrocephalus. An ultrasound examination revealed hyperechogenic lenses, microphthalmia, hypotelorism, retrognathia, mild ventriculomegaly, absence of the cavum septum pellucidum, and short stature. Amniocentesis and further microarray analysis revealed normal chromosomal copy numbers including the gene B3GALTL In utero mort fetalis occurred at the 23rd gestational week. Ultrasound and fetal autopsy findings were suggestive of Peters plus syndrome, but the absence of the B3GALTL gene mutation made the diagnosis Peters plus-like syndrome. Obstetricians should consider Peters plus-like syndrome with prenatal detection of ocular anomalies along with craniofacial and skeletal anomalies with the absence of B3GALTL gene mutation.Article Citation - WoS: 19Citation - Scopus: 22Chaperonin (hsp60) and Annexin-2 Are Candidate Biomarkers for Non-Small Cell Lung Carcinoma(Lippincott Williams & Wilkins, 2017) Agababaoglu, Ismail; Onen, Ahmet; Demir, Ayse Banu; Aktas, Safiye; Altun, Zekiye; Ersoz, Hasan; Sanli, AydinBackground: Lung cancer is responsible of 12.4% and 17.6% of all newly diagnosed cancer cases and mortality due to cancer, respectively, and 5-year survival rate despite all improved treatment options is 15%. This survival rate reaches 66% in the Stage 1 and surgically treated patients. Early diagnosis which could not be definitely and commonly achieved yet is extremely critical in obtaining high survival rate in this disease. For this reason; proteomic differences were evaluated using matrix assisted laser desorption ionization (MALDI) mass spectrometry in the subgroups of lung adenocarcinoma and squamous cell carcinoma. Methods: Fresh tissue samples of 36 malignant cases involving 83.3% (n= 30) men and 16.7% (n= 6) women patients were distributed into 2 groups as early and end stage lung cancer and each group were composed of subgroups including 18 squamous cell carcinoma (9 early stage cases, 9 end stage cases) and 18 adenocarcinoma cases (9 early stage cases, 9 end stage cases). The fresh tissues obtained from the tumoral and matched normal sites after surgical intervention. The differences in protein expression levels were determined by comparing proteomic changes in each patient. Results: In the subgroups of advanced stage adenocarcinoma; tumoral tissue revealed differences in expression of 2 proteins compared with normal parenchymal tissue. Of those; difference in protein expression in heat shock protein 60 (HSP60) was found statistically significant (P= 0.0001). Subgroups of early and advanced stage squamos cell carcinoma have differed in certain 20 protein expression of normal tissue and diseased squamos cell carcinoma. Of those, increased protein expression level of only annexin-2 protein was found statistically significant (P= 0.002). No significant difference was detected in early and advanced stage protein expressions of the tumoral tissues in the subgroups of adenocarcinoma and squamous cell carcinoma. Conclusions: We conclude that with respect to early diagnosis of lung cancer that HSP60 and annexin-2 proteins are the important biomarkers in the subgroups of adenocarcinoma and squamous cell carcinoma. We also consider that these 2 proteins are molecules which may provide critical contribution in evaluation of prognosis, metastatic potential, response to treatment, and in establishment of differential diagnosis between adenocarcinoma and squamous cell carcinoma.Article Citation - WoS: 1Citation - Scopus: 1Toll-Interacting Protein May Affect Doxorubicin Resistance in Hepatocellular Carcinoma Cell Lines(Springer, 2023) 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.Article Citation - WoS: 17Citation - Scopus: 18Evidence for Mutations in Sars-Cov Italian Isolates Potentially Affecting Virus Transmission(Wiley, 2020) Benvenuto, Domenico; Demir, Ayse Banu; Giovanetti, Marta; Bianchi, Martina; Angeletti, Silvia; Pascarella, Stefano; Cauda, RobertoItaly 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.
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