Bioengineering / Biyomühendislik

Permanent URI for this collectionhttps://hdl.handle.net/11147/4529

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Now showing 1 - 10 of 39
  • Annotation
    On-Chip 3d Cell Culture Platform for Tumor Modeling and Drug Screening
    (2022) Yıldırım, Özüm; Arslan Yıldız, Ahu
  • Article
    Citation - Scopus: 3
    Development of Chrono-Spectral Gold Nanoparticle Growth Based Plasmonic Biosensor Platform
    (Elsevier, 2024) Sözmen, Alper Baran; Elveren, Beste; Erdoğan, Duygu; Mezgil, Bahadır; Baştanlar, Yalın; Yıldız, Ümit Hakan; Arslan Yıldız, Ahu
    Plasmonic sensor platforms are designed for rapid, label-free, and real-time detection and they excel as the next generation biosensors. However, current methods such as Surface Plasmon Resonance require expertise and well-equipped laboratory facilities. Simpler methods such as Localized Surface Plasmon Resonance (LSPR) overcome those limitations, though they lack sensitivity. Hence, sensitivity enhancement plays a crucial role in the future of plasmonic sensor platforms. Herein, a refractive index (RI) sensitivity enhancement methodology is reported utilizing growth of gold nanoparticles (GNPs) on solid support and it is backed up with artificial neural network (ANN) analysis. Sensor platform fabrication was initiated with GNP immobilization onto solid support; immobilized GNPs were then used as seeds for chrono-spectral growth, which was carried out using NH2OH at varied incubation times. The response to RI change of the platform was investigated with varied concentrations of sucrose and ethanol. The detection of bacteria E.coli BL21 was carried out for validation as a model microorganism and results showed that detection was possible at 102 CFU/ml. The data acquired by spectrophotometric measurements were analyzed by ANN and bacteria classification with percentage error rates near 0% was achieved. The proposed LSPR-based, label-free sensor application proved that the developed methodology promises utile sensitivity enhancement potential for similar sensor platforms. © 2024 The Author(s)
  • Conference Paper
    3d Printing-Assisted Fabrication of Microfluidic Pneumatic Valves
    (IEEE, 2023) Keleş, Şeyda; Karakuzu, Betül; Tekin, Hüseyin Cumhur
    Pneumatic valves have a crucial place in the fluidic control in microfluidic systems. Pneumatic valves containing polydimethylsiloxane (PDMS) membrane structures are used in microfluidic systems such as cell separation, and cell manipulation due to their flexible structure, and ease of production. This study demonstrates the rapid and straightforward fabrication of pneumatic valve structures using PDMS membranes, achieved through the utilization of 3D-printed molds. As a result of our experiments, we observed valve closure in a fluidic channel with a height of 150 μm. This closure was achieved by utilizing 400 μm × 800 μm PDMS membrane with a thickness of 66 μm positioned between the fluidic and control channels, while applying 1.5 bar of pressure to the control channel. When the pressure is removed, the opening time of the valve is only 0.02 s, and this response time allows rapid valving function. The presented valve fabrication strategy would allow easy and low-cost production of sophisticated microfluidic chips. © 2023 IEEE.
  • Book Part
    Astragalus sp.
    (CRC Press, 2023) Yakuboğulları, Nilgün; Bedir, Erdal
    Astragalus is one of the largest genera in Turkey and is widely distributed worldwide. The phytochemical studies on Turkish Astragalus species have presented 112 new compounds besides 63 known compounds. The overriding basis for biological activity studies is the traditional use of Astragalus roots in the Southeastern Region of Turkey to cure leukemia. As the isolated compounds did not show cytotoxic properties, a hypothesis that the biological activity of Astragalus saponins might result from the activation of the immune system came up. While Astragalus polysaccharides are used for their strong immunomodulatory activities in Chinese medicine, there are a few articles revealing the immunostimulatory properties of Astragalus saponins. Here, we summarized the compounds isolated from Turkish Astragalus species and concentrated on the immunomodulatory activities of these compounds to put forward their potential as saponin-based vaccine adjuvants. © 2024 selection and editorial matter, Ufuk Koca-Caliskan; individual chapters, the contributors.
  • Article
    Citation - Scopus: 11
    Μdacs 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 Cumhur
    Circulating 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)
  • Article
    Modelling Genotoxic Effects of Metal Oxide Nanoparticles Using Qsar Approach
    (2022) Öksel Karakuş, Ceyda
    We investigated the application of structure-activity relationship approaches to underpin structural properties that potentially control the genotoxic potential of 9 different metal oxide nanoparticles (CuO, ZnO, NiO, SiO2, TiO2, CeO2, Fe2O3, Fe3O4 and Co3O4). In particular, we compiled a pool of quantum-mechanical, experimental and periodic table-driven descriptors and explored their distinctive contribution to the measured activity (genotoxicity). We first employed a clustered heatmap and parallel coordinates plot for visual exploration of the clusters and outliers of the data and finding corresponding responsible physicochemical descriptors. We then investigated the strength (and direction) of the relationship among descriptors and between descriptors and genotoxicity using similarity metrics. By using orthogonal projections to latent structures (OPLS), we were able to quantify the relative contribution of each descriptor to the genotoxicity of metal oxide nanoparticles. Our results suggested that zeta potential, the ratio of core electrons to valence electrons, Fermi energy and electronegativity were significant predictors of genotoxicity. Such computer-assisted approaches hold considerable promise for maximizing the use of accumulated data in nanotoxicology, prioritizing nanoparticles for further testing and filling data gaps required for hazard assessment processes.
  • Book Part
    Citation - Scopus: 2
    Bioprinting of Hydrogels for Tissue Engineering and Drug Screening Applications
    (Elsevier, 2022) Özmen, Ece; Yıldırım, Özüm; Arslan Yıldız, Ahu
    In tissue engineering, the 3-dimensional (3D) bioprinting method that enables the production of 3D structures by combining bioinks and cells has become one of the most promising technique. Over the last few years, 3D cell culture models gained importance in the development of disease model and drug development studies. The successful production of the 3D structures by 3D bioprinting mostly depends on the properties of the bioink to be used. Hydrogels, which are natural or synthetic polymers, are generally preferred as bioink materials with their high swelling ability, biocompatibility, biodegradability, and easy gelation ability. The convenience of hydrogels for varied bioprinting applications make them proper bioink materials for bioprinting of artificial tissues, tumor models, and tissue grafts. Bioprinting of functional tissues is successfully performed for years, and hydrogels are utilized as bioink in bone, vascular, neural, cartilage, cardiac, skin tissue engineering, and drug screening. In this chapter, bioprinting methodology, bioinks, hydrogel bioinks, and their applications are discussed in detail. © 2023 Elsevier Inc. All rights reserved.
  • Book Part
    Citation - Scopus: 3
    Tissue Engineering Applications of Marine-Based Materials
    (Springer, 2022) Polat, Hürriyet; Zeybek, Nuket; Polat, Mehmet
    Tissue engineering is a promising approach in replacing or improving tissues lost or has become nonviable due to disease or trauma by the use of scaffold materials by combining engineering and biochemical/physicochemical methods. Its purpose is to create suitable matrices that support cell differentiation and proliferation toward the formation of new and functional tissue. Marine-based natural compounds are potential scaffold feedstock material in tissue engineering owing to their biocompatibility and biodegradability while providing excellent biochemical/physicochemical properties. Numerous application areas and various fabrication routes techniques described in the literature attest to the importance of these materials in tissue regeneration. This review has been carried to merge the information from a large number of studies on the marine-based scaffold materials in tissue engineering into a coherent summary. © The Editor(s) (if applicable) and The Author(s), under exclusive license to Springer Nature Singapore Pte Ltd. 2022.
  • Conference Object
    Lots and Loop-Mediated Isothermal Amplification-Based Biosensing Using Cloud-Enabled Features
    (IEEE, 2022) Bayındır, Taha; Değirmenci, Mehmet; Ergenç, Ali Fuat; Elitaş, Meltem
    Internet-of-Things technology (IoTs) have accelerated biosensor applications in all fields. Loop-mediated isothermal amplification (LAMP)-based biosensor technologies in conjunction with smartphone detection have been adequate to cover the demands of mobile diagnostics. The ease of use, affordability, portability, high sensitivity, flexibility, and specificity demands of point-of-care detection can be achieved by low-cost electronic components, 3-dimensional printing technologies, capturing images of calorimetrically detected readouts made our system a promising approach for real-time point-of-detection in the field. In this study, we implemented a cloud service to our LAMP-based biosensor. We previously performed bacteria detection using colony-based LAMP device and now distributed the optical readouts of the assay using smartphones. We transferred the obtained image and results of the assays through cloud. Our user-friendly interface simplifies the data processing, it directly digitized the readouts and eliminates the need of data interpretation.
  • Book Part
    Noncoding Way of the Metastasis
    (Elsevier, 2022) Göker Bağca, Bakiye; Kuşoğlu, Alican; Çeşmeli, Selin; Biray Avcı, Çığır
    According to the World Health Organization statistics, the second leading cause of death globally is cancer. Together with this, metastasis is viewed as the leading cause of cancer death in patients with the disease due to the lack of treatment modalities for malignant tumors. One of the key mechanisms related to cancer metastasis is the epithelial-mesenchymal transition which enables epithelial cancer cells to gain mesenchymal cancer cell properties with elevated migration and invasion capacity that make it easy to spread distant tissues and survive from harsh conditions. Studies indicate that metastatic cancer cells have a gene expression signature that ensures those cells have increased migratory capacity as well as increased survival rate in circulation. Recently, the relationship of metastasis with two types of noncoding RNAs (ncRNAs), microRNAs (miRNAs), and long noncoding RNAs (lncRNAs) has been getting attention. In this chapter, the role of miRNAs and lncRNAs and treatment strategies regarding the role of ncRNAs in metastasis biology will be evaluated.