Bioengineering / Biyomühendislik
Permanent URI for this collectionhttps://hdl.handle.net/11147/4529
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Conference Object Deep Convolutional Neural Networks for Viability Analysis Directly From Cell Holograms Captured Using Lensless Holographic Microscopy(The Chemical and Biological Microsystems Society (CBMS), 2019) Delikoyun, Kerem; Çine, Ersin; Anıl İnevi, Müge; Özçivici, Engin; Özuysal, Mustafa; Tekin, Hüseyin CumhurCell viability analysis is one of the most widely used protocols in the fields of biomedical sciences. Traditional methods are prone to human error and require high-cost and bulky instrumentations. Lensless digital inline holographic microscopy (LDIHM) offers low-cost and high resolution imaging. However, recorded holograms should be digitally reconstructed to obtain real images, which requires intense computational work. We introduce a deep transfer learning-based cell viability classification method that directly processes the hologram without reconstruction. This new model is only trained once and viability of each cell can be predicted from its hologram. © 2019 CBMS-0001.Article Citation - WoS: 13Citation - Scopus: 15Cytotoxic Tolerance of Healthy and Cancerous Bone Cells To Anti-Microbial Phenolic Compounds Depend on Culture Conditions(Humana Press, 2019) Karadaş, Özge; Meşe, Gülistan; Özçivici, EnginCarnosol and carnosic acid are polyphenolic compounds found in rosemary and sage with known anti-oxidant, anti-inflammatory, and anti-microbial properties. Here, we addressed the potential use of carnosol and carnosic acid for in vitro bone tissue engineering applications, specifically depending on their cytotoxic effects on bone marrow stromal and stem cells, and osteosarcoma cells in monolayer and 3D cultures. Carnosol and carnosic acid displayed a bacteriostatic effect on Gram-positive bacteria, especially on S. aureus. The viability results indicated that bone marrow stromal cells and bone marrow stem cells were more tolerant to the presence of carnosol compared to osteosarcoma cells. 3D culture conditions increased this tolerance further for healthy cells, while not affecting the cytotoxic potential of carnosol for osteosarcoma cells. Carnosic acid was found to be more cytotoxic for all cell types used in the study. Results suggest that phenolic compounds might have potential use as anti-microbial and anti-carcinogenic agents for bone tissue engineering with further optimization for controlled release.Article Citation - WoS: 8Citation - Scopus: 11Application of Low Intensity Mechanical Vibrations for Bone Tissue Maintenance and Regeneration(TÜBİTAK, 2016) Ölçüm, Melis; Baskan, Öznur; Karadaş, Özge; Özçivici, EnginPhysical exercise is beneficial for bone tissue health, yet its usage is limited for preventing osteoporosis. Even though natural for the bone tissue from development to homeostasis, mechanical loads present with a multitude of physical parameters, including amplitude, duration, frequency, and distribution. Utilizing the most beneficial parameters of mechanical loads may potentiate a nonpharmaceutical tool for biotechnology to prevent and treat bone loss related to aging, bedrest, sedentary lifestyles, weightlessness, and other diseases. Low intensity vibrations (LIVs) consist of mechanical loads with amplitudes smaller than loads prescribed by habitual activity, with a higher frequency. In this review, literature covering LIV signal application on bone tissue and cellular and molecular level is presented. Studies indicate that LIV signals are safe, anabolic, and anticatabolic for skeletal tissue and are of great significance in regenerative medicine applications.Article Citation - WoS: 79Citation - Scopus: 93Magnetic Force-Based Micro Fluidic Techniques for Cellular and Tissue Bioengineering(Frontiers Media S.A., 2018) Yaman, Sena; Anıl İnevi, Müge; Özçivici, Engin; Tekin, Hüseyin CumhurLive cell manipulation is an important biotechnological tool for cellular and tissue level bioengineering applications due to its capacity for guiding cells for separation, isolation, concentration, and patterning. Magnetic force-based cell manipulation methods offer several advantages, such as low adverse effects on cell viability and low interference with the cellular environment. Furthermore, magnetic-based operations can be readily combined with microfluidic principles by precisely allowing control over the spatiotemporal distribution of physical and chemical factors for cell manipulation. In this review, we present recent applications of magnetic force-based cell manipulation in cellular and tissue bioengineering with an emphasis on applications with microfluidic components. Following an introduction of the theoretical background of magnetic manipulation, components of magnetic force-based cell manipulation systems are described. Thereafter, different applications, including separation of certain cell fractions, enrichment of rare cells, and guidance of cells into specific macro- or micro-arrangements to mimic natural cell organization and function, are explained. Finally, we discuss the current challenges and limitations of magnetic cell manipulation technologies in microfluidic devices with an outlook on future developments in the field.Conference Object Role of Connexin 32 on Gap Junctions in Breast Cancer Cells With Varying Metastatic Potential.(American Society for Cell Biology, 2017) Uğur, Deniz; Özçivici, Engin; Meşe, Gülistan[No abstract available]Conference Object Investigating the Role of Connexin 32 in Cell Cycle, Cell Viability and Epithelial To Mesenchymal Transition of Normal Breast and Breast Cancer Cells(American Society for Cell Biology, 2017) Adak, Aslı; Özçivici, Engin; Meşe, Gülistan[No abstract available]Conference Object Genetic Determinants of Musculoskeletal Adaptations To Unloading and Reloading(Institute of Electrical and Electronics Engineers Inc., 2019) Özçivici, Engin; Judex, StefanLack of weight bearing is one of the most critical limitations for long term health of bone tissue in space missions. In this study, we performed a series of Quantitative Trait Locus (QTL) analysis of musculoskeletal traits to define genomic modulators adaptations to mechanical unloading and subsequent reloading using a genetically heterogeneous (F2 BALBxC3H) female mouse population. The identified regions on genome contain genes that regulate musculoskeletal adaptations to weightlessness and further studies may help to categorize individuals that are at risk for greater tissue loss during weightlessness and/or low tissue recovery during reambulation.Conference Object Citation - WoS: 5Citation - Scopus: 8Lensless Digital In-Line Holographic Microscopy for Space Biotechnology Applications(Institute of Electrical and Electronics Engineers Inc., 2019) Delikoyun, Kerem; Çine, Ersin; Anıl İnevi, Müge; Özuysal, Mustafa; Özçivici, Engin; Tekin, Hüseyin CumhurBiomechanical changes at cellular level can dramatically affect living organisms in both aviation and space applications. Weightlessness induces morphological alteration of cells, which leads to tissue loss. Therefore, scientists have been studying the effect of weightlessness using cell culture based biological experiments using conventional microscopes. However, strict requirements regarding cost, weight and functionality limit the use of conventional microscopes in space environment. Lensless digital in-line holographic microscopy enables to use low-weight, low-cost and robust elements, such as a light emitting diode (LED), an aperture and an imaging sensor, instead of bulky, expensive and fragile optical elements, such as lenses, mirrors and filters. This technology offers a high field of view compared to conventional microscopes without affecting the resolution and it is also suitable for remote sensing applications with automated imaging capabilities. Here, we present a portable digital in-line holographic microscopy platform that allows to visualize cells and to analyze their viability in a microfluidic chip. The platform offers microscopic imaging with 1.55 mu m spatial resolution, 21.7 mm(2) field of view and image coloring capability. This platform could potentially play an important role in space biotechnology applications by enabling low-cost, high-resolution and portable monitoring of cells.Conference Object Citation - WoS: 7Citation - Scopus: 7Cell Separation With Hybrid Magnetic Levitation-Based Lensless Holographic Microscopy Platform(Institute of Electrical and Electronics Engineers Inc., 2019) Delikoyun, Kerem; Yaman, Sena; Anıl İnevi, Müge; Özçivici, Engin; Tekin, Hüseyin CumhurSeparation of target cells in a heterogeneous solution is of great importance for clinical studies especially for immunology and oncology. Separated cells can be used for diagnostic applications ranging from whole blood counting to isolation of circulating tumor cells (CTC) for personalized medicine. Recent separation technologies rely on labelling and identifying target cells with variety of labelling principle such as fluorescence or magnetic tags. However, they require labor-intensive processes, long analysis time, and expensive chemical reagents and instrumentation. Hence, their usage is limited to well-equipped centralized laboratories. There is a need for a rapid, sensitive, low-cost and automated cell separation technology to disseminate usage of this technology even in rural areas. Magnetic levitation is a powerful cell separation method, which distinguishes cells based on their levitation heights depending on cell density. However, magnetic levitation-based separation technologies require traditional, bulky and expensive microscopes for analysis. Lensless digital inline holographic microscopy (LDIHM) systems are composed of a simple illumination system containing an LED, a pinhole, and an imaging sensor for high-resolution microscopic imaging, which eliminates needs of highly fragile and expensive optics as in traditional microscopy. Here, we introduced a novel hybrid and portable cell separation platform, where magnetic levitation technology is integrated with LDIHM system for automated analysis of cell levitation heights. Using this platform, three different cell lines are successfully separated. Live and dead cells having distinguished levitation heights can be also identified in the platform.Article Citation - WoS: 18Citation - Scopus: 17Cnt Incorporated Polyacrilonitrile/Polypyrrole Nanofibers as Keratinocytes Scaffold(Trans Tech Publications, 2019) İnce Yardımcı, Atike; Aypek, Hande; Öztürk, Özgür; Yılmaz, Selahattin; Özçivici, Engin; Meşe, Gülistan; Selamet, YusufPolypyrrole (PPy) is an attractive scaffold material for tissue engineering with its non-toxic and electrically conductive properties. There has not been enough information about PPy usage in skin tissue engineering. The aim of this study is to investigate biocompatibility of polyacrilonitrile (PAN)/PPy nanofibrous scaffold for human keratinocytes. PAN/PPy bicomponent nanofibers were prepared by electrospinning, in various PPy concentrations and with carbon nanotube (CNT) incorporation. The average diameter of electrospun nanofibers decreased with increasing PPy concentration. Further, agglomerated CNTs caused beads and disordered parts on the surface of nanofibers. Biocompatibility of these PAN/PPy and PAN/PPy/CNT scaffolds were analyzed in vitro. Both scaffolds provided adhesion and proliferation of keratinocytes. Nanofiber diameter did not significantly influence the morphology of cells. However, with increasing number of cells, cells stayed among nanofibers and this affected their shape and size. In this study, we demonstrated that PAN/PPy and PAN/PPy/CNT scaffolds enabled the growth of keratinocytes, showing their biocompatibility.