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Atçeken, Nazente

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Nazente

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Atçeken

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Atçeken, Nazente

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2022 - 20235

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    Identification of hub genes and key pathways between celiac and crohn's diseases via bioinformatics tools
    (2022) Gül, Kozalak; Köksal, Özgül Rıza; Department of Molecular Biology and Genetics; Atçeken, Nazente; PhD Student; Department of Molecular Biology and Genetics; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); College of Sciences; N/A
    Background: Chronic inflammatory diseases are the long-term response of the organism to any stimulus. Crohn's (CD) and Celiac (CeD) diseases are among chronic inflammatory diseases, and both cause chronic inflammation in the intestines. Both diseases are caused by polygenic, environmental, and lifestyle risk factors. Inflammation can perpetuate disease and cause it to become chronic. For this reason, CD and CeD that choose the intestine as the target organ may trigger each other. Although the relationship between these diseases is widely mentioned in the literature, scanty knowledge and research have been done on the immune mechanisms of these inflammatory diseases. Aim: This study aimed to determine hub genes, transcription factors-miRNAs, and protein-chemical interaction networks shared between CD and CeD. Methods: The NCBI-GEO datasets were downloaded and analyzed in GEO2R to identify differentially expressed genes (DEGs). STRING tool for Protein -Protein Interaction (PPI) and NetworkAnalyst tool were used for Gene Set Enrichment Analysis (GSEA), Transcription factor (TF) -miRNA Coregulatory Networks, and Protein-Chemical Interactions. Results and Discussion: GSE11501 and GSE3365 datasets were utilized to recognize 54 DEGs in CD, and CeD. 13 of these commonly expressed genes were defined as hub genes. GSEA has indicated that these genes are associated with immune system processes, cellular defense response, proteolysis, and apoptosis. KAT6A and SPI1 are transcription factors that direct the continuity of intestinal epithelial cells. Antirheumatic agents and Methotrexate are likely to be used to treat these diseases. Conclusions: In conclusion, we think that delayed-type hypersensitivity resulting from epitope propagation is a common immune mechanism of CD and CeD. Given the increasing prevalence of both CD and CeD in the population, it is clear that more studies are needed to understand the shared pathogenesis and overlapping immune mechanisms of these diseases.
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    3D bioprinted glioma models
    (Iop Publishing Ltd, 2022) N/A; N/A; N/A; N/A; N/A; N/A; N/A; Department of Mechanical Engineering; Yığcı, Defne; Sarabi, Misagh Rezapour; Üstün, Merve; Atçeken, Nazente; Sokullu, Emel; Önder, Tuğba Bağcı; Taşoğlu, Savaş; Undergraduate Student; PhD Student; PhD Student; Researcher; Faculty Member; Faculty Member; Faculty Member; Department of Mechanical Engineering; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); School of Medicine; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; N/A; School of Medicine; School of Medicine; College of Engineering; N/A; N/A; N/A; N/A; 163024; 184359; 291971
    Glioma is one of the most malignant types of cancer and most gliomas remain incurable. One of the hallmarks of glioma is its invasiveness. Furthermore, glioma cells tend to readily detach from the primary tumor and travel through the brain tissue, making complete tumor resection impossible in many cases. To expand the knowledge regarding the invasive behavior of glioma, evaluate drug resistance, and recapitulate the tumor microenvironment, various modeling strategies were proposed in the last decade, including three-dimensional (3D) biomimetic scaffold-free cultures, organ-on-chip microfluidics chips, and 3D bioprinting platforms, which allow for the investigation on patient-specific treatments. The emerging method of 3D bioprinting technology has introduced a time- and cost-efficient approach to create in vitro models that possess the structural and functional characteristics of human organs and tissues by spatially positioning cells and bioink. Here, we review emerging 3D bioprinted models developed for recapitulating the brain environment and glioma tumors, with the purpose of probing glioma cell invasion and gliomagenesis and discuss the potential use of 4D printing and machine learning applications in glioma modelling.
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    Point-of-care diagnostic platforms for loop-mediated isothermal amplification
    (Wiley-V C H Verlag Gmbh, 2023) Alseed, Muhammad Munzer; Yetişen, Ali K; N/A; N/A; Department of Mechanical Engineering; Atçeken, Nazente; Dabbagh, Sajjad Rahmani; Taşoğlu, Savaş; Researcher; PhD Student; Faculty Member; Department of Mechanical Engineering; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); KU Arçelik Research Center for Creative Industries (KUAR) / KU Arçelik Yaratıcı Endüstriler Uygulama ve Araştırma Merkezi (KUAR); N/A; Graduate School of Sciences and Engineering; College of Engineering; N/A; N/A; 291971
    The loop-mediated isothermal amplification (LAMP) method is one of the Nucleic acid amplification tests (NAATs) that allows for the amplification of target regions without using a thermal cycle. With its unique primer design, LAMP ensures the rapid replication of the targeted DNA region with high specificity and high efficiency. LAMP technology is used for diagnostic purposes in pathogen detection due to its ease of use, low cost, and simplicity without requiring complex equipment. A wide range of LAMP diagnostic platforms have been developed for applications in bacteria, virus, and parasitic pathogen detection. Herein, the methodology of LAMP technology and its applications in pathogen detection and SNP genotyping and mutation detection are discussed. Point-of-care (PoC) LAMP platforms designed with the principles of microfluidic chip technology, including LAMP-on-a-chip, paper-based LAMP, and smartphone-based LAMP applications have been elaborated. LAMP technology represents a fast, robust, and reliable diagnostic platform for point-of-care testing.
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    PublicationOpen Access
    CRISPR-Cas-Integrated LAMP
    (Multidisciplinary Digital Publishing Institute (MDPI), 2022) N/A; Department of Mechanical Engineering; Özdalgıç, Berin; Taşoğlu, Savaş; Yığcı, Defne; Atçeken, Nazente; PhD Student; Faculty Member; Department of Mechanical Engineering; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); KU Arçelik Research Center for Creative Industries (KUAR) / KU Arçelik Yaratıcı Endüstriler Uygulama ve Araştırma Merkezi (KUAR); Graduate School of Sciences and Engineering; College of Engineering; School of Medicine; N/A; 291971; N/A; N/A
    Pathogen-specific point-of-care (PoC) diagnostic tests have become an important need in the fight against infectious diseases and epidemics in recent years. PoC diagnostic tests are designed with the following parameters in mind: rapidity, accuracy, sensitivity, specificity, and ease of use. Molecular techniques are the gold standard for pathogen detection due to their accuracy and specificity. There are various limitations in adapting molecular diagnostic methods to PoC diagnostic tests. Efforts to overcome limitations are focused on the development of integrated molecular diagnostics by utilizing the latest technologies available to create the most successful PoC diagnostic platforms. With this point of view, a new generation technology was developed by combining loop-mediated isothermal amplification (LAMP) technology with clustered regularly interspaced short palindromic repeat (CRISPR)-associated (CRISPR-Cas) technology. This integrated approach benefits from the properties of LAMP technology, namely its high efficiency, short turnaround time, and the lack of need for a complex device. It also makes use of the programmable function of CRISPR-Cas technology and the collateral cleavage activity of certain Cas proteins that allow for convenient reporter detection. Thus, this combined technology enables the development of PoC diagnostic tests with high sensitivity, specificity, and ease of use without the need for complicated devices. In this review, we discuss the advantages and limitations of the CRISPR/Cas combined LAMP technology. We review current limitations to convert CRISPR combined LAMP into pathogen-specific PoC platforms. Furthermore, we point out the need to design more useful PoC platforms using microfabrication technologies by developing strategies that overcome the limitations of this new technology, reduce its complexity, and reduce the risk of contamination.
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    PublicationOpen Access
    Emerging applications of electrochemical impedance spectroscopy in tear film analysis
    (Multidisciplinary Digital Publishing Institute (MDPI), 2022) Department of Mechanical Engineering; Taşoğlu, Savaş; Özdalgıç, Berin; Gül, Münire; Atçeken, Nazente; Uygun, Zihni Onur; Faculty Member; PhD Student; Other; Department of Mechanical Engineering; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); KU Arçelik Research Center for Creative Industries (KUAR) / KU Arçelik Yaratıcı Endüstriler Uygulama ve Araştırma Merkezi (KUAR); College of Engineering; 291971; 323683; N/A; N/A; N/A
    Human tear film, with a flow rate of 1–3 µL/min, is a rich bodily fluid that transmits a variety of metabolites and hormones containing proteins, lipids and electrolytes that provide clues about ocular and systemic diseases. Analysis of disease biomarkers such as proteins, mRNA, enzymes and cytokines in the tear film, collected by noninvasive methods, can provide significant results for sustaining a predictive, preventive and personalized medicine regarding various diseases such as glaucoma, diabetic retinopathy, keratoconus, dry eye, cancer, Alzheimer’s disease, Parkinson’s disease and COVID-19. Electrochemical impedance spectroscopy (EIS) offers a powerful technique for analyzing these biomarkers. EIS detects electrical equivalent circuit parameters related to biorecognition of receptor–analyte interactions on the electrode surface. This method is advantageous as it performs a label-free detection and allows the detection of non-electroactive compounds that cannot be detected by direct electron transfer, such as hormones and some proteins. Here, we review the opportunities regarding the integration of EIS into tear fluid sampling approaches.