Browsing by Author "Temirci, Elif Sena"

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Open Access
Assessing the genetic impact of Enterococcus faecalis infection on gastric cell line MKN74
(Springer, 2021-12) Türk, Seyhan; Türk, Can; Temirci, Elif Sena; Malkan, Umit Yavuz; Ucar, Gulberk; Ozguven, Sukru Volkan
Purpose Enterococcus faecalis (E. faecalis) is an important commensal microbiota member of the human gastrointestinal tract. It has been shown in many studies that infection rates with E. faecalis in gastric cancer significantly increase. It has been scientifically proven that some infections develop during the progression of cancer, but it is still unclear whether this infection factor is beneficial (reduction in metastasis) or harmful (increase in proliferation, invasion, stem cell-like phenotype) of the host. These opposed data can significantly contribute to the understanding of cancer progress when analyzed in detail. Methods The gene expression data were retrieved from Array Express (E-MEXP-3496). Variance, t test and linear regression analysis, hierarchical clustering, network, and pathway analysis were performed. Results In this study, we identified altered genes involved in E. faecalis infection in the gastric cell line MKN74 and the relevant pathways to understand whether the infection slows down cancer progression. Twelve genes corresponding 15 probe sets were downregulated following the live infection of gastric cancer cells with E. faecalis. We identified a network between these genes and pathways they belong to. Pathway analysis showed that these genes are mostly associated with cancer cell proliferation. Conclusion NDC80, NCAPG, CENPA, KIF23, BUB1B, BUB1, CASC5, KIF2C, CENPF, SPC25, SMC4, and KIF20A genes were found to be associated with gastric cancer pathogenesis. Almost all of these genes are effective in the proliferation of cancer cells, especially during the infection process. Therefore, it is hypothesized that downregulation of these genes may affect gastric cancer pathogenesis by reducing cell proliferation. And, it is predicted that E. faecalis infection may be an important factor for gastric cancer.
Open Access
Current community transmission and future perspectives on the COVID-19 process
(TÜBİTAK, 2021-03) Türk, S.; Türk, C.; Malkan, Ü. Y.; Temirci, Elif Sena; Peker, M. Ç.; Haznedaroĝlu, İ. C.
Background/aim: COVID-19 syndrome due to the SARS-CoV-2 virus is a currently challenging situation ongoing worldwide. Since the current pandemic of the SARS-CoV-2 virus is a great concern for everybody in the World, the frequently asked question is how and when the COVID-19 process will be concluded. The aim of this paper is to propose hypotheses in order to answer this essential question. As recently demonstrated, SARS-CoV-2 RNAs can be reverse-transcribed and integrated into the human genome. Our main hypothesis is that the ultimate aim of the SARS-CoV-2 virus is the incorporation to human genome and being an element of the intestinal virobiota. Materials and methods: We propose that the SARS-CoV-2 genomic incorporation to be a part of human virobiota is essentially based on three pathobiological phases which are called as the ‘induction’, ‘consolidation’, and ‘maintenance phases’. The phase of ‘recurrence’ complicates any of these three disease phases based on the viral load, exposure time, and more contagious strains and/or mutants. We have performed the ‘random walk model’ in order to predict the community transmission kinetics of the virus. Results: Chimerism-mediated immunotherapy at the individual and community level with the help of vaccination seems to be the only option for ending the COVID-19 process. After the integration of SARS-CoV-2 virus into the human genome via the induction, consolidation, and maintenance phases as an element of intestinal virobiota, the chimerism would be concluded. The ‘viral load’, the ‘genomic strain of the SARS-CoV-2’, and ‘host immune reaction against the SARS-CoV-2’ are the hallmarks of this long journey. Conclusion: Elucidation of the functional viral dynamics will be helpful for disease management at the individual- and community based long-term management strategies.
Open Access
The impact of JAK/STAT inhibitor ruxolitinib on the genesis of lymphoproliferative diseases
(TÜBİTAK, 2019-04) Türk, Can; Okay, M.; Türk, S.; Temirci, Elif Sena; Javad, Osama; Aksu, S.; Sayınalp, N.; Haznedaroğlu, İ. C.
Background/aim: Ruxolitinib, a JAK/STAT signaling pathway inhibitor targeted drug, has been approved for the controlling of disease symptoms and splenomegaly in patients with myeloproliferative neoplastic diseases. Recently, it has been proposed that ruxolitinibinduced JAK/STAT pathway inhibition in myelofibrosis is associated with an elevated frequency of aggressive B-cell lymphomas. However, the biological basis and significance of this pharmacobiological adverse event is unknown. The aim of this bioinformatics study is to detect any possible confounding effects of ruxolitinib on the genesis of lymphoproliferative disorders. Materials and methods: The gene expression data were retrieved from the E-MTAB-783 Cancer Genome Project database. Gene expression data for all available genes in 26 cell lines belonging to various types of lymphomas were chosen for use in this in silico analysis. Results: We identified genes that were significant in developing resistance to ruxolitinib in lymphoma cell lines. Conclusion: Based on the results of our present study, ruxolitinib may potentially lead to the pathological expression of the transcription factors important in lymphoma genesis, neoplastic commitment on the progenitor lymphoid cells, inhibition of repressor transcriptions protective for lymphoma development, inhibition of apoptosis, promotion of neoplastic proliferation, transcriptional activation, and proliferation of malignant neoplastic B cells.
Open Access
In vitro analysis of the renin–angiotensin system and inflammatory gene transcripts in human bronchial epithelial cells after infection with severe acute respiratory syndrome coronavirus
(SAGE, 2020) Türk, C.; Türk, S.; Temirci, Elif Sena; Malkan, Ü. Y.; Haznedaroğlu, İ. C.
Introduction: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a recently identified coronavirus family member that triggers a respiratory disease similar to severe acute respiratory syndrome coronavirus (SARS-CoV). SARS-CoV and SARS-CoV-2 are very similar to each other in many respects, such as structure, genetics, and pathobiology. We hypothesized that coronaviruses could affect pulmonary tissues via integration with the critical immune genes after their interaction with renin–angiotensin system (RAS) elements. The aim of the present bioinformatics study was to assess expression changes of the RAS and non-RAS genes, particularly immune response genes, in the lung epithelial cells after infection with SARS-CoV. Methods: Linear regression, hierarchical clustering, pathway analysis, and network analysis were performed using the E-GEOD-17400 data set. Results: The whole-genome expression data of the lung epithelial cells infected with SARS-CoV for 12, 24, and 48 hours were analyzed, and a total of 15 RAS family and 29 immune genes were found to be highly correlated with the exposure time to the virus in the studied groups. Conclusion: RAS genes are important at the initiation of the infections caused by coronavirus family members and may have a strong relationship with the exchange of immune genes in due course following the infection.
Open Access
Interferon-gene family alterations following the SARS-Cov infection in association with iron metabolism and lymphoid biology
(Akademi Doktorlar Yayınevi, 2021) Malkan, U. Y.; Türk, S.; Türk, C.; Temirci, Elif Sena; Köker, İdil; Haznedaroĝlu, I. C.
Interferon (IFN) family has a significant impact on both SARS-CoV and SARS-CoV-2. The aim of this current bioinformatics study is to assess IFN-gene family alterations following the SARS-CoV infection in association with the iron metabolism and lymphoid biology. Gene expression data of human bronchial epithelial cells treated with SARS-CoV for 12, 24, 48 hours were obtained from Array Express (GSE17400). In order to use the obtained data in other targeted analyses,the raw data were normalized by robust multisequence analysis in accordance with the procedure in the Affy package in R. These data consist of 23344 genes (54675 probe sets). In addition, each gene has three repeated expression data values for 12, 24, 48 hours, respectively. For the 48 hours group,positive regulations of the natural killer (NK) cell activation and NK cell-mediated cytotoxicity, as well as hematopoietic stem cells proliferation,were found to be more significant regard to their nominal p-value, family-wise error rate, and false discovery rate (q-value) calculated by gen set enrichment analysis. The gene sets with nominal (NOM) p-value < 0.01, false discovery rate (FDR) q-value ≤ 1, and familywise error rate (FWER) < 1 considered as significantly correlate between compared groups. Our study exhibited that important IFN genes (IFNAR2, IFNA10, IFNA1, IFNLR1, IFNA21, IFNA4, IFNL2, IFNL1, IFNA16, IFNA17) behave like immune genes that show low expression in 12 hours virus exposure, unlike demonstrate high gene expression at 48 hours virus exposure. Likewise, three IFN genes (IFNAR1, IFNGR1, IFNG) have high expression levels at the 12 hours exposure and low expressions at the 48 hours virus expression. All of these interferon genes expression were highly correlated and statistically significant (p< 0.05, pearson r-value > 0.8) with exposure time to the virus. These results suggest that hematopoietic stem cell proliferation pathway is affected by the viral SARS-CoV infection.
Embargo
Longevity and circadian rhythm in Caenorhabditis elegans: the impact of lithium chloride
(2024-06) Temirci, Elif Sena
Lithium chloride (LiCl) is a popular treatment for various neurological disorders, especially bipolar disorders. While its complete mechanism of action remains partially elucidated, LiCl has been found to support new memory formation by triggering the construction of new neurons, reducing senescence, and regulating the circadian rhythm, particularly in bipolar patients, where it counteracts their abnormally fast biological clock. The circadian rhythm is vital in determining efficiency, understanding energy consumption, and biochemical balance for all organisms. This rhythm includes regulating body functions by the day/night cycle. Caenorhabditis elegans (C. elegans) is one of the most robust organisms for modeling circadian rhythm, although it lives in the soil. Therefore, by employing C. elegans as a model system, valuable insights could be gained for these complex processes. This study aims to elucidate the complex relationship between LiCl, circadian rhythms, and longevity, as disruptions in these pathways are implicated in neurodegenerative diseases and age-related cognitive and motor decline. In this project, white light was employed to manipulate the circadian rhythm in C. elegans, with one group additionally receiving LiCl treatment in addition to light exposure. The study focused on longevity, response to environmental factors, and circadian rhythm. To elucidate the effect on longevity, lifespan measurements showed that LiCl treatment extended the lifespan of C. elegans under both light and dark conditions, with a shorter lifespan observed in the light. Additionally, when comparing the effect of specific developmental time points, the signs of aging appeared later in the dark compared to the light. The differential gene expression of longevity genes suggested that LiCl treatment could impact gene expression, particularly the age-1 gene, but not the daf-16 gene. Furthermore, the response to environmental changes was examined imilarly and it was observed that C. elegans responded to the circadian rhythm disruption caused by light and LiCl administration. In conclusion, this study suggests that LiCl treatment has the potential to mitigate the adverse effects of circadian rhythm disruptions and reverse the aging process of C. elegans.
Restricted
Savaş ortamında hoşgörü ve yardımlaşma: 1974 Kıbrıs Barış Harekatı örneği
(Bilkent University, 2018) Özer, Ali; Kınık, Can; Önen, Çağan; Temirci, Elif Sena; Taşkan, Hilal
Kıbrıs Barış Harekâtı, adada Türklerin Rumlar tarafından maruz bırakıldığı toplumsal baskı ve şiddete son vermeyi amaçlayarak gerçekleştirildi. Esasında Kıbrıs Türklerinin Rumlara karşı toplum olma bilincinin getirmiş olduğu müsamahaya ve empatiye dayanan tavrına cevaben, Enosis hayali çerçevesinde adadaki etnik çeşitliliğe son vermeyi planlayan ve buna bağlı olarak Türkleri adadan göndermeyi hedefleyen politikalar, toplumsal huzursuzluğun büyümesine sebep oldu. Bu çalışmada, bu zorlu zamanları yaşayarak tecrübe etmiş kişilerle yapılan röportajlar, her ne kadar savaşlardan dolayı oluşan şiddet ve kaos ortamı olsa da Kıbrıs Türklerinin ve Rumlarının birbirlerine karşı sergilemiş olduğu anlayış ve hoşgörü politikaları örneklendirilerek belirtildi.