Molecular Biology and Genetics / Moleküler Biyoloji ve Genetik
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Book Structural Defense of Plants and Pathogenesis(01. Izmir Institute of Technology, 2023) Ekinci, Berkay; Ekinci, BerkayThe major challenge in today s world is ensuring an adequate food supply for the growing global population. Achieving this goal requires the development of crops by using sustainable agricultural strategies in ecologically suitable areas (Jan et al. 2011; Doğanlar et al. 2023). However, plant diseases, which are caused by various pathogens such as bacteria, fungi, viruses, nematodes, and herbivores, pose a significant threat to crop quality and yield. Fortunately, plants have several preexisting and induced defense and immune mechanisms to protect themselves against biotic and abiotic stresses (Jones et al. 2006; Freeman et al. 2008). This review aims to provide information on phytopathogens, the steps of pathogenesis, plants’ pre-existing structural defense mechanisms against pathogenesis, and more. It is aimed at broadening the reader's knowledge and perspective by providing a wide range of examples, from simple to complex. I hope that this review will be a good start for enlightening and inspiring all curious scientists who, like me, are enthusiastic about this field.Article Citation - Scopus: 11Μdacs Platform: a Hybrid Microfluidic Platform Using Magnetic Levitation Technique and Integrating Magnetic, Gravitational, and Drag Forces for Density-Based Rare Cancer Cell Sorting(Elsevier, 2023) Keçili, Seren; Yılmaz, Esra; Özçelik, Özge Solmaz; Anıl İnevi, Müge; Günyüz, Zehra Elif; Yalçın Özuysal, Özden; Özçivici, Engin; Tekin, Hüseyin CumhurCirculating tumor cells (CTCs) are crucial indicators of cancer metastasis. However, their rarity in the bloodstream and the heterogeneity of their surface biomarkers present challenges for their isolation. Here, we developed a hybrid microfluidic platform (microfluidic-based density-associated cell sorting (µDACS) platform) that utilizes density as a biophysical marker to sort cancer cells from the population of white blood cells (WBCs). The platform utilizes the magnetic levitation technique on a microfluidic chip to sort cells based on their specific density ranges, operating under a continuous flow condition. By harnessing magnetic, gravitational, and drag forces, the platform efficiently separates cells. This approach involves a microfluidic chip equipped with a microseparator, which directs cells into top and bottom outlets depending on their levitation heights, which are inversely proportional to their densities. Hence, low-density cancer cells are collected from the top outlet, while high-density WBCs are collected from the bottom outlet. We optimized the sorting efficiency by varying the flow rates, and concentrations of the sorting medium's paramagnetic properties using standard densities of polymeric microspheres. To demonstrate the platform's applicability, we performed hybrid microfluidic sorting on MDA-MB-231 human breast cancer cells and U-937 human monocytes. The results showed efficient sorting of rare cancer cells (≥100 cells/mL) from serum samples, achieving a sorting efficiency of ∼70% at a fast-processing speed of 1 mL h−1. This label-free approach holds promise for rapid and cost-effective CTC sorting, facilitating in-vitro diagnosis and prognosis of cancer. © 2023 The Author(s)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.Article Determination of Resistance Levels To Clavibacter Michiganensis Subsp. Michiganensis in Some Solanum Species(Ege Tarımsal Araştırma Enstitüsü, 2022) Frary, Anne; Şanver, Utku; Akköse Baytar, Asena; Özaktan, Hatice; Doğanlar, SamiClavibacter michiganensis subsp. michiganensis (Cmm), is a devastating bacterial disease agent causing bacterial wilt and canker in tomatoes. There is no definitive solution to prevent yield losses by Cmm in tomatoes. Moreover, there is currently no commercially successful Cmm resistant tomato cultivar on the market. Therefore, we aimed to determine the tolerance level of some tomato accessions to Cmm in the present study. For this purpose, we screened seven tomato accessions representing four species (Solanum arcanum, S. habrochaites, S. pennellii, and S. peruvianum) from Peru, Ecuador, and Mexico against the highly virulent isolates Cmm-244 and Cmm-9. A root immersion method was used to identify new sources of resistance to this important disease. Two accessions, S. habrochaites LA1777, and S. arcanum LA2157 were found to be moderate and highly tolerant, respectively, and could serve as tolerance resources for tomato breeding in Türkiye. These materials can also be investigated more extensively to determine their intrinsic Cmm tolerance mechanism.Book Part Citation - Scopus: 5Epitranscriptomics Changes the Play: M6a Rna Modifications in Apoptosis(Springer, 2022) Akçaöz, Azime; Akgül, BünyaminApoptosis is a form of programmed cell death that is essential for cellular and organismal homeostasis. Any irregularities that disturb the balance between apoptosis and cell survival have severe implications, such as improper development or life-threatening diseases. Thus, it is highly critical to maintain a proper rate of apoptosis throughout development. In fact, several complex transcriptional and posttranscriptional mechanisms exist in eukaryotes to critically regulate the rate of apoptotic processes. Recent studies suggest that not only RNA sequences but also their modifications, such as m6A methylation, play a fundamental role in these transcriptional and posttranscriptional processes. A specific set of proteins, called writer, eraser, and reader of m6A marks, modulate the rate of apoptosis by determining the m6A repertoire and the fate of certain transcripts associated with apoptosis. In this Review, we will cover the dynamic m6A RNA modifications and their impact on modulation of apoptosis.Editorial Citation - Scopus: 1Lessons From a Ten-Year Journey: Building a Student-Driven Computational Biology Society Across Turkey(F1000 Research, 2022) Kaya, Yasin; Karakulak, Tülay; Saylan, Cemil Can; Gür, E. Ravza; Tatlıdil, Engin; Güleşen, Sevilay; Betül Dinçaslan, Fatma; Dönertaş, Handan MelikeThe Regional Student Group Turkey (RSG-Turkey) is officially associated with the International Society for Computational Biology (ISCB) Student Council (SC). At the RSG-Turkey, we aim to contribute to the early-career researchers in computational biology and bioinformatics fields by providing opportunities for improving their academic and technical skills in the field. Over the last ten years, we have built a well-known student-driven academic society in Turkey that organizes numerous events every year and continues to grow with over 650 current members. Celebrating the 10th anniversary of RSG-Turkey, in this communication, we share our experiences, five main lessons we learned, and the steps to establish a long-standing academic community: having a clear mission, building a robust structure, effective communication, turning challenges into opportunities, and building collaborations. We believe that our experiences can help students and academics establish long-standing communities in fast-developing areas like bioinformatics.Conference Object Citation - WoS: 3Citation - Scopus: 4Deep Learning Based Segmentation Pipeline for Label-Free Phase-Contrast Microscopy Images(IEEE, 2020) Ayanzadeh, Aydın; Yalçın Özuysal, Özden; Okvur, Devrim Pesen; Önal, Sevgi; Töreyin, Behçet Uğur; Ünay, DevrimThe segmentation of cells is necessary for biologists in the morphological statistics for quantitative and qualitative analysis in Phase-contrast Microscopy (PCM) images. In this paper, we address the cell segmentation problem in PCM images. Deep Neural Networks (DNNs) commonly is initialized with weights from a network pre-trained on a large annotated data set like ImageNet have superior performance than those trained from scratch on a small dataset. Here, we demonstrate how encoder-decoder type architectures such as U-Net and Feature Pyramid Network (FPN) can be improved by an alternative encoder which pre-trained on the ImageNet dataset. In particular, our experimental results confirm that the image descriptors from ResNet-18 are highly effective in accurate prediction of the cell boundary and have higher Intersection over Union (IoU) in comparison to the classical U-Net and require fewer training epochs.Conference Object Assessment of Cell Cycle and Viability of Magnetic Levitation Assembled Cellular Structures(IEEE, 2020) Anıl İnevi, Müge; Ünal, Yağmur Ceren; Yaman, Sena; Tekin, H. Cumhur; Meşe, Gülistan; Meşe, GülistanLabel-free magnetic levitation is one of the most recent Earth-based in vitro techniques that simulate the microgravity. This technique offers a great opportunity to biofabricate scaffold-free 3-dimensional (3D) structures and to study the effects of microgravity on these structures. In this study, self-assembled 3D living structures were fabricated in a paramagnetic medium by magnetic levitation technique and effects of the technique on cellular health was assessed. This magnetic force-assisted assembly system applied here offers broad applications in several fields, such as space biotechnology and bottom-up tissue engineering.Master Thesis Investigation of the Pathology of Brain Derived Endothelial Cells in In-Vitro Hypoxia Models(01. Izmir Institute of Technology, 2021) Erdemli, Kısmet Tuğçe; Tosun, ÇiğdemThe blood brain barrier (BBB) is a vital structure that protects brain homeostasis. Endothelial cells (EC) have a significant role in regulating the BBB structure and function. Several studies have revealed the association of SUR1-TRPM4 channels that regulate this secondary damage of CNS injuries. After the activation of the channel, Na+ influx causes depolarization, cell swelling (edema) and ultimately oncotic cell death. Hypoxia inducing factor (HIF) transcription factor that has been reported to activate more than 100 genes to adapt to a hypoxic condition. Once Hif1-⍺ is translocated into the nucleus, it can dimerize with HIF1-ß to produce HIF that is critical in hypoxic conditions and regulate cell cycle arrest or cell death pathways. Hypoxia can occur in an O2 dependent and independent manner. In this study, CoCl2 and hypoxia chamber which was cost-effective and reliable were optimized. Cellular death was calculated with Trypan blue staining in this novel hypoxia chamber model and compared with CoCl2 models. In addition, morphological changes were observed in microscopic analysis. Hif1-⍺, caspase-3 and NF-κB translocation to the nucleus localization were quantified. Cell viability was different between the CoCl2 model and novel hypoxia chamber model at 24 hours. The cellular death increased with CoCl2 exposure, where no change was noted in the hypoxia chamber model. Time dependent Hif1-⍺ upregulation was also demonstrated that peaked at 12-hours. Finally, NF-κB translocation into the nucleus was significantly increased at 24 hours of hypoxia exposure. The results reveal that the inflatable hypoxia chamber model could be reliably used to mimic hypoxia in an in-vitro setting. Hif1-⍺ activated in a time dependent manner, along with NF-κB. The upregulation of these transcription factors can ultimately affect the cellular death mechanisms differentlyBook Part Citation - Scopus: 86The Role of Mirna in Cancer: Pathogenesis, Diagnosis, and Treatment(Humana Press, 2022) Uzuner, Erez; Ulu, Gizem Tuğçe; Gürler, Sevim Beyza; Baran, YusufCancer is also determined by the alterations of oncogenes and tumor suppressor genes. These gene expressions can be regulated by microRNAs (miRNA). At this point, researchers focus on addressing two main questions: “How are oncogenes and/or tumor suppressor genes regulated by miRNAs?” and “Which other mechanisms in cancer cells are regulated by miRNAs?” In this work we focus on gathering the publications answering these questions. The expression of miRNAs is affected by amplification, deletion or mutation. These processes are controlled by oncogenes and tumor suppressor genes, which regulate different mechanisms of cancer initiation and progression including cell proliferation, cell growth, apoptosis, DNA repair, invasion, angiogenesis, metastasis, drug resistance, metabolic regulation, and immune response regulation in cancer cells. In addition, profiling of miRNA is an important step in developing a new therapeutic approach for cancer. © 2022, Springer Science+Business Media, LLC, part of Springer Nature.