TR Dizin İndeksli Yayınlar Koleksiyonu / TR Dizin Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/20.500.14365/4
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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: 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 Citation - Scopus: 2Behavioral Immune System and Trypophobia(Klinik Psikiyatri Dergisi, 2022) Ozturk, Suleyman; Ceylan, Deniz; Demir, Ayse Banu; Kazdagli, Hasan; Erdeniz, BurakPathogens, which are the source of infectious diseases, have imposed a strong selection pressure on human evo-lution as one of the most important causes of human death during the natural selection process. As a result of this, it is assumed that a variety of adaptations have evolved against infection threats and one of these adap-tations is the physiological immune system. However, activation of the physiological immune system can be quite costly for organisms in some cases, and therefore it has been recently proposed in evolutionary psychology that an adaptive system called behavioral immune sys-tem may have evolved in association with the proactive functional processes against pathogen threats. Furthermore, it was hypothesized that a number of psy-chopathologies might develop as a result of maladaptive processes affecting the functionality of this system, and one of these psychopathologies might be trypophobia. Trypophobia refers to a psychological disorder in which individuals experience aversion and disgust at excessive levels toward clusters of small objects such as holes and bumps. Following this, the current review was estab-lished within the framework of three distinct goals. Firstly, this review aimed to discuss the evolutionary basis and mechanisms of the behavioral immune system. Secondly, the review aimed to discuss the characteristic features and the etiological explanations of trypophobia. Finally, the review aimed to discuss how potential changes in the behavioral immune system might lead to the development of trypophobia.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.Article Multidisciplinary Case-Based Small Group Discussions To Integrate Basic Medical Sciences With Clinical Situations(Walter De Gruyter Gmbh, 2020-09-18) Şemin, Makbule İlgi; Ersil Soysal, Dilek; Seval Çelik, Yasemin; Hayran, Murvet; Demir, Ayse Banu; Ozkaya, Ali Burak; İnan, Sevinç; Akdoğan, Gül; Semin, Ilgi; Soysal, Dilek Ersil; Seval-Celik, Yasemin; Güner, Gül AkdoganObjectives Integration of the basic medical sciences with clinical medicine motivates medical students by showing how the fundamental concepts they have learned will come into their future practice. In this context, we created clinical integration sessions (CIS) in our first-year medical curriculum. Methods The instructors of different disciplines wrote the clinical scenarios together. The scenarios were discussed in five sessions with 39 first-year students. The first session's scenario consisted of four brief anemia cases. The next four sessions included a single case, according to the feedback of the students. Students formed groups of 7-8 participants. In the first 2 h, the scenarios were discussed in the groups and questions were answered by the students. In the third hour, the instructors answered the questions together with the students. After the first CIS, written feedback obtained from the students via a survey. Results The survey provided positive feedback on the benefits of active learning within small group discussions, and most of the students thought that their background was sufficient to solve the cases, with some literature search. Conclusion The scenarios, which provide multidisciplinary integration of basic medical sciences and clinical medicine, can be useful educational materials.