Molecular Biology and Genetics / Moleküler Biyoloji ve Genetik
Permanent URI for this collectionhttps://hdl.handle.net/11147/9
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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.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 Assessment of Undergraduate Health Students' Perception and Satisfaction on Training and Participation in Community Health Outreach(Springer, 2023) Adegbore, Abidemi Kafayat; Adedokun, Amudatu Ambali; Adegoke, Juliet Ifeoluwa; Lawal, Maruf Ayobami; Oke, MuseAimThe need to improve training of health professionals has increased in recent years due to increasing frequencies of public health events. Consequently, a descriptive cross-sectional survey was carried out to determine the level of satisfaction and knowledge acquired by undergraduate students in the health sciences during a community health outreach program.Subject and methodsStudents were invited to complete an online-administered questionnaire (consisting of both open- and closed-ended questions) to assess their perceptions and experiences on the community health outreach program. Additionally, the survey was carried out to assess the quality of training provided and obtain suggestions for further improvements. Responses were collected and analysed using Microsoft Excel.ResultsMost respondents (>83%) reported satisfaction with the community diagnosis and community intervention briefing and training sessions. All respondents reported familiarity with standard community health outreach instruments and were capable of identifying environmental health risk factors that may contribute to the spread of communicable diseases. Interestingly, respondents reported greater appreciation of health challenges faced by rural communities. However, respondents expressed dissatisfaction with the duration of the outreach program (24%) and funding (15%).ConclusionAlthough respondents reported overall satisfaction with the organization and execution of the health outreach program, certain aspects of the program were deemed unsatisfactory. Despite the shortcomings, we believe that our student-centred learning strategy is readily adaptable for training future healthcare professionals and improving health literacy of rural communities, particularly in sub-Saharan Africa.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.Article Citation - WoS: 139Granulocytic Sarcoma: a Systematic Review(e-Century Publishing Corporation, 2013) Yılmaz, Asu Fergün; Saydam, Güray; Şahin, Fahri; Baran, YusufGranulocytic sarcoma also called myeloid sarcoma is an extramedullary tumor of immature granulocytic cells. It is a rare entity, and mostly accompanied by acute myeloid leukemia. It is observed during the course of myeloproliferative disorders especially in chronic myeloid leukemia and myelodysplastic syndromes. In some rare circumstances, it is detected before clinical signs of leukemia or other diseases. When the bone marrow biopsy reveals no other hematologic malignancies, the granulocytic sarcoma is described as nonleukemic, primary or isolated. It is observed at any part of the body but the most common locations are soft tissues, bone, peritoneum and lymph nodes. Presenting signs or symptoms are mainly due to mass effect of the tumor and dysfunction of the organ, or the tissue that is affected. The diagnosis is performed by biopsy of the tumor. The tumor consists of immature granulocytic cells, which could be documented by H&E, immunohistochemistry, and flow cytometric methods. Fluorescence in-situ hybridization and molecular analysis are also performed. The optimal time and type of treatment is not clear. Surgery could be an option especially for tumors, which cause organ dysfunction and/or obstruction. Systemic treatment should be considered in all patients because without systemic treatment, relapses and progression to acute myeloid leukemia is the ultimate fate of the disease in many cases. Cytarabine-containing remission-induction chemotherapies have been the most applied therapeutic strategies, but it is not clear whether the consolidation therapies are required or not, and what kind of regimens are appropriate. The role of hematopoietic stem cell transplantation (HSC) as a consolidation regimen is not clear, but, after the relapse of the disease with or without bone marrow involvement, HSC transplantation should be considered in suitable patients after the reinduction performed by AML chemotherapies. There is only limited data about the role of radiotherapy in these patients. It could be used in patients with relapsed disease, organ dysfunction which should be quickly relieved and inadequate response to chemotherapy. The effect of radiotherapy on overall survival is not known. New prospective studies and clinical trials are needed to generate guidelines for the treatment of primary granulocytic sarcomas.Article Citation - WoS: 15Changes in Molecular Biology of Chronic Myeloid Leukemia in Tyrosine Kinase Inhibitor Era(e-Century Publishing Corporation, 2013) Cömert, Melda; Baran, Yusuf; Saydam, GürayChronic myeloid leukemia (CML) is a clonal myeloproliferative disease characterized by a reciprocal translocation between long arms of chromosomes 9 and 22 t(9; 22) that generates the BCR-ABL fusion gene. If left untreated, newly diagnosed chronic phase CML patients finally progress to accelerated and blastic phase. After the introduction of tyrosine kinase inhibitors (TKIs), treatment strategies of CML changed dramatically. However, the development of resistance to TKIs started to create problems over time. In this review, the current information about CML biology before and after imatinib mesylate treatment is summarized.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 differentlyPatent Three Dimensional Microfluidic Device That Determines Metastatic Capacity and Homing Choices(European Patent Office, 2014)The invention provides a device that mimics the in vivo tumor microenvironment comprising different cell types, matrices, biological molecules and chemicals. All steps of metastasis, namely, angiogenesis, matrix invasion, cell migration, intravasation, circulation, extravasation and new tumor formation, in addition to homing choices of cancer cells can simultaneously and jointly be investigated using the said microfluidic device. The design of the device with multiple adjacent channels comprising 3D cell-laden or cell free matrices(24, 25, 26, 27, 28, 29) neighboring a flow channel (30) allows determination of metastatic capacity and homing choices of cancer cells.