Molecular Biology and Genetics / Moleküler Biyoloji ve Genetik
Permanent URI for this collectionhttps://hdl.handle.net/11147/9
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Book Part Citation - Scopus: 1Automated Analysis of Phase-Contrast Optical Microscopy Time-Lapse Images: Application To Wound Healing and Cell Motility Assays of Breast Cancer(Elsevier, 2023) Erdem, Yusuf Sait; Ayanzadeh, Aydın; Mayalı, Berkay; Balıkçı, Muhammed; Belli, Özge Nur; Uçar, Mahmut; Yalçın Özuysal, Özden; Pesen Okvur, Devrim; Önal, Sevgi; Morani, Kenan; Iheme, Leonardo Obinna; Töreyin, Behçet UğurThis chapter describes a workflow for analyzing phase-contrast microscopy (PCM) data from two fundamental types of biomedical assays: assays for cell motility and assays for wound healing. The workflow of the analysis is composed of the methods for acquiring, restoring, segmenting, and quantifying biomedical data. In the literature, there have been separate methods aimed at specific stages of PCM data analysis. Nonetheless, there has never been a complete workflow for all stages of analysis. This work is an innovation that proposes an end-to-end workflow for image pre-processing, deep learning segmentation, tracking, and quantification stages in cell motility and wound healing assay analyses. The findings indicate that domain knowledge can be used to make simple but significant improvements to the results of cutting-edge methods. Furthermore, even for deep learning-based methods, pre-processing is clearly a necessary step in the workflow. © 2023 Elsevier Inc. All rights reserved.Book Part Citation - Scopus: 4Epigenetics of Breast Cancer: Dna Methylome and Global Histone Modifications(Springer, 2016) Meşe, Gülistan; Yalçın Özuysal, ÖzdenBreast cancer, a heterogeneous disease comprised of tumors with different histological characteristics and clinical outcomes, is the leading cause of cancer deaths in women. Heterogeneous nature of the breast cancer demands delicate approaches to diagnose and follow the most appropriate strategy for clinical management. Based on microarray analysis of mRNA expression, four main molecular subtypes were identified: (a) luminal A, (b) luminal B, (c) basal-like, and (d) ERBB2(+). Even though molecular subtypes provided novel insights into our understanding of breast cancer heterogeneity, there is still room for improvement for better diagnostic, prognostic and therapeutic approaches. In this sense, epigenetics, specifically DNA methylation and histone modifications, have emerged as prominent candidates since several epigenetic factors were observed to be recurrently mutated in cancers including breast cancer. Recent advances in the field implicated that DNA methylation profiles and histone modifications are strongly associated with breast tumor subtypes and patient prognosis. Therefore, understanding contributions of epigenetics to breast cancer biology will lead to better diagnostic and prognostic strategies and will enable development of novel therapeutic approaches. © Springer International Publishing Switzerland 2016.Article Citation - WoS: 5Citation - Scopus: 7The Roles of Antiapoptotic Sphingosine Kinase-1 and Glucosylceramide Genes in Drug Induced Cell Death of Mcf-7 Breast Cancer Cells(Zerbinis Medical Publications, 2011) Güçlüler, Gözde; Pişkin, Özden; Baran, YusufPurpose: Sphingolipids are important signaling molecules mediating cell survival, proliferation, cell cycle regulation and apoptosis. Ceramide is the most vital sphingolipid which induces growth arrest, senescence, and apoptosis. In this study, we aimed to determine the roles of sphingosine kinase- 1 (SK-1) and glucosylceramide synthase (GCS) genes in paclitaxel, doxorubicin, tamoxifen, cyclophosphamide and docetaxel induced apoptosis in human MCF-7 breast cancer cells. Methods: IC50 values (drug concentration inhibiting cell growth by 50%) of the anticancer agents were calculated using XTT cell proliferation assay. Changes in mitochondrial membrane potential (MMP) were determined using JC-1 assay kit. Changes in the mRNA levels of SK-1 and GCS genes were measured by using RT-PCR technique. Results: The results demonstrated significant decrease in cellular proliferation and increase in loss of MMP in a dose-dependent manner. Paclitaxel, doxorubicin, tamoxifen, cyclophosphamide and docetaxel application downregulated SK-1 expression while paclitaxel, tamoxifen, cyclophosphamide and docetaxel but not doxorubicin downregulated GCS comparing to untreated control cells. Conclusion: These results show for the first time that these agents induce apoptosis in MCF-7 cells by downregulating the antiapoptotic SK-1 and GCS genes that may result in accumulation of apoptotic ceramides. © 2011 Zerbinis Medical Publications.