Molecular Biology and Genetics / Moleküler Biyoloji ve Genetik

Permanent URI for this collectionhttps://hdl.handle.net/11147/9

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Now showing 1 - 10 of 11
  • Book
    Structural Defense of Plants and Pathogenesis
    (01. Izmir Institute of Technology, 2023) Ekinci, Berkay; Ekinci, Berkay
    The 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.
  • Review
    A review on the removal of viruses by adsorption
    (Gazi University, 2023) Eren, Muhammet Şakir Abdullah; Tanaydın, Elif Sila; Arslanoğlu, Hasan; Çiftçi, Harun
    The potential dangers of Covid-19 (SARS-CoV-2 Infection), which spread to almost all countries from Wuhan, China's Hubei province in 2020, have been the focus of attention of scientists worldwide Serious impact processes of Covid-19, ranging from pneumonia to severe acute respiratory infections and from kidney failure to death, continue to threaten millions of people. Isolation of pandemic species is of great importance for the development of appropriate treatment protocols in emerging viral infections. For this, it is necessary to develop existing methods as well as new methods. Viruses do not exist in living form in nature and they need other creatures to transfer their genetic material. In this respect, water resources and air appear as the most important means of transmission. Adsorption processes for the transmission means can be applied to prevent the spread of viruses and to inactivate them. In this review, the interactions of viruses with various adsorbents containing carbonaceous, oxidized, porous anf metal organic framework materials were examined. Electrostatic interactions were found to be more effective in target types of adsorbing processes of adsorbents used in water and air purification. Since the virus surface carries various organic functional groups, it is seen that it will interact with different adsorbents electrostatic and in this way they can be removed and both isolated and rendered ineffective. We think that our study will contribute to effective solutions to prevent the spread of other pathogens, including coronaviruses, by adsorption processes to be applied to air and water sources and to disinfect the specified transmission means.
  • Book Part
    Citation - Scopus: 1
    Automated 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 Uğur
    This 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, Muse
    AimThe 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.
  • Research Project
    Pamukta Lif Verimi ve Kalite Karakterleri için Kantitatif Karakter Lokus Analizleri
    (2020) Doğanlar, Sami
    Pamuk ıslahı çalısmalarında rutin olarak pedigrisi belli ebevenylerin melezlenmesi, açılım populasyonlarının olusturulması ve fenotipe dayalı seleksiyon islemleri ile yürütülen çalısmalar pamuk gen havuzunu fark edilir bir sekilde daraltmıs ve bunun neticesinde, günümüzdeki pamuk çesitleri arasındaki genetik çesitliligin çok düsük düzeylerde kalmasına neden olmustur. Pamuk ıslah çalısmalarında yıllardır aynı ıslah metodunun kullanılması, aynı ebevenylerin sürekli olarak ıslah çalısmalarında donor anaç olarak kullanımı ve pamuk ıslahçılarının adapte olmamıs germplazmları kullanmak istememeleri yıllar süren klasik ıslahın sonucu olarak pamuk genomunda çesitligin azalmasına neden olmustur. Bu durumda, yapılan melezlemelerde rekombinantların ortaya çıkarılma sansını azaltmıstır. Dolayısıyla, pamuk ıslah çalısmalarında fenotipik ve genotipik olarak karakterize edilmis germplazmların olusturulması; hem lif verimi ve kalitesi bakımından önemli karakterlerin genetik kontrollerinin anlasılması ve marköre dayalı seleksiyon çalısmalarının baslatılması ve hemde olusturulacak kombinasyon ıslahı çalısmalarında kullanılacak anaçların seçilmesi açısında önemlidir. Önerilen projede lif karakterleri bakımından iki yıl süreyle incelenmis degisik kademelerdeki RIL populasyonlarında moleküler markör analizleri yapılmıstır. Böylece, fenotipik ve genotipik olarak yüksek düzeyde çesitlilige sahip olan pamuk genotipleri belirlenmis ve ayrıca iliskilendirme analizleri ile agronomik karakterler bakımından iliskili genom bölgeleri (markörler) tespit edilmistir.
  • 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, Sami
    Clavibacter 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.
  • Conference Object
    Citation - WoS: 3
    Citation - Scopus: 4
    Deep 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, Devrim
    The 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
    Citation - Scopus: 2
    Yara İyileşmesi Mikroskopi Görüntü Serilerinin Otomatik Analizi - Bir Ön-çalışma
    (IEEE, 2020) Mayalı, Berkay; Şaylığ, Orkun; Yalçın Özuysal, Özden; Pesen Okvur, Devrim; Töreyin, Behçet Uğur; Ünay, Devrim
    Collective cell analysis from microscopy image series is important for wound healing research. Computer-based automation of such analyses may help in rapid acquisition of reliable and reproducible results. In this study phase -contrast optical microscopy image series of an in-vitro wound healing essay is manually delineated by two experts and its analysis is realized, traditional image processing and deep learning based approaches for automated segmentation of wound area are developed and their perlOrmance comparisons are carried out.
  • 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, Gülistan
    Label-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, Çiğdem
    The 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 differently