Bioengineering / Biyomühendislik

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

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  • Conference Object
    A Glucuronoxylan-Based Bio-Ink Development: Characterization and Application
    (Wiley, 2023) Yıldırım, Ömer; Arslan Yıldız, Ahu
    Bioprinting is a trending technique that enables the fabrication of three­dimensional (3D) constructs in designed shapes and with desired properties. Bio­inks are one of the most significant components of bioprinting and the successful fabrication of 3D bioprinted constructs mostly depends on the features of bio­inks that would be used. New generation bio­inks that are soft and viscous enough, printable under low pressure, stable in cell culture, and have fast gelation mechanisms are ideal to be used in current bioprinting techniques. Hydrocolloids have said features and have similar properties to native ECM structures. Hence bio­inks that are developed from hydrocolloids can be utilized for mimicking of ECM structure of soft tissues. Polysaccharide­based hydrocolloids are ideal bio­ink candidates with their high waterholding capacity and biocompatibility. Here, a glucuronoxylan­based new­generation bio­ink was developed, and its printability was evaluated for 3D bioprinting applications. The glucuronoxylan­based hydrocolloid was obtained by water extraction of quince seeds and its utilization in bioprinting was investigated. Bio­ink characterization was done by FTIR and mechanical analysis. Bioprinting parameters were optimized assessing uniformity, pore factor, and shape fidelity. Then, the characterization of bioprinted constructs was performed by pore angle measurement, water­holding capacity analysis, protein adsorption, and cell viability assays. Bioprinted structures have high mechanical strength, suitable protein adsorption behavior, and water­holding capacity as high as 20­fold of its own weight, which is higher than other hydrogels that were used in soft tissue engineering. Moreover, the cell viability results of fibroblast cells in the bio­ink were high for long­term culture. In conclusion, findings show that the developed glucuronoxylan­based bio­ink is a biocompatible and promising bio­ink material for further tissue engineering applications.
  • Conference Object
    Citation - WoS: 1
    Immunomodulatory Mechanisms of Astragalus Saponins
    (Wiley, 2021) Yakuboğulları, Nilgün; Çağır, Ali; Bedir, Erdal; Sağ, Duygu
  • Article
    Citation - WoS: 6
    Citation - Scopus: 6
    Functional Characterization of a Novel Cyp119 Variant To Explore Its Biocatalytic Potential
    (Wiley, 2021) Sakallı, Tuğçe; Sürmeli, Nur Başak
    Biocatalysts are increasingly applied in the pharmaceutical and chemical industry. Cytochrome P450 enzymes (P450s) are valuable biocatalysts due to their ability to hydroxylate unactivated carbon atoms using molecular oxygen. P450s catalyze reactions using nicotinamide adenine dinucleotide phosphate (NAD(P)H) cofactor and electron transfer proteins. Alternatively, P450s can utilize hydrogen peroxide (H2O2) as an oxidant, but this pathway is inefficient. P450s that show higher efficiency with peroxides are sought after in industrial applications. P450s from thermophilic organisms have more potential applications as they are stable toward high temperature, high and low pH, and organic solvents. CYP119 is an acidothermophilic P450 from Sulfolobus acidocaldarius. In our previous study, a novel T213R/T214I (double mutant [DM]) variant of CYP119 was obtained by screening a mutant library for higher peroxidation activity utilizing H2O2. Here, we characterized the substrate scope; stability toward peroxides; and temperature and organic solvent tolerance of DM CYP119 to identify its potential as an industrial biocatalyst. DM CYP119 displayed higher stability than wild-type (WT) CYP119 toward organic peroxides. It shows higher peroxidation activity for non-natural substrates and higher affinity for progesterone and other bioactive potential substrates compared to WT CYP119. DM CYP119 emerges as a new biocatalyst with a wide range of potential applications in the pharmaceutical and chemical industry.
  • Article
    Citation - WoS: 22
    Citation - Scopus: 26
    Magnetic Levitation Assisted Biofabrication, Culture, and Manipulation of 3d Cellular Structures Using a Ring Magnet Based Setup
    (Wiley, 2021) Anıl İnevi, Müge; Delikoyun, Kerem; Meşe Özçivici, Gülistan; Tekin, Hüseyin Cumhur; Özçivici, Engin
    Diamagnetic levitation is an emerging technology for remote manipulation of cells in cell and tissue level applications. Low-cost magnetic levitation configurations using permanent magnets are commonly composed of a culture chamber physically sandwiched between two block magnets that limit working volume and applicability. This work describes a single ring magnet-based magnetic levitation system to eliminate physical limitations for biofabrication. Developed configuration utilizes sample culture volume for construct size manipulation and long-term maintenance. Furthermore, our configuration enables convenient transfer of liquid or solid phases during the levitation. Before biofabrication, we first calibrated/ the platform for levitation with polymeric beads, considering the single cell density range of viable cells. By taking advantage of magnetic focusing and cellular self-assembly, millimeter-sized 3D structures were formed and maintained in the system allowing easy and on-site intervention in cell culture with an open operational space. We demonstrated that the levitation protocol could be adapted for levitation of various cell types (i.e., stem cell, adipocyte and cancer cell) representing cells of different densities by modifying the paramagnetic ion concentration that could be also reduced by manipulating the density of the medium. This technique allowed the manipulation and merging of separately formed 3D biological units, as well as the hybrid biofabrication with biopolymers. In conclusion, we believe that this platform will serve as an important tool in broad fields such as bottom-up tissue engineering, drug discovery and developmental biology.
  • Article
    Citation - WoS: 2
    Citation - Scopus: 2
    Cloning, Expression, and Characterization of a Novel Sericin-Like Protein
    (Wiley, 2022) Bostan, Fatmanur; Sürmeli, Nur Başak
    Silk consists of two proteins called fibroin and sericin. While fibroin is used in the textile industry and has various biomaterial applications, sericin has been considered as waste material until recently. Sericin is a multicomponent protein and it has important properties such as biocompatibility, biodegradability, cryoprotectivity, and antioxidant. Sericin from silkworm cocoons can be obtained by chemical, enzymatic, and heat treatment methods. However, sericin obtained with these treatment methods is not of consistent and high quality. Moreover, the exposure of sericin to harsh conditions during extraction leads to inconsistencies in the composition and structure of the sericin obtained. The inconsistencies in sericin structure and composition decrease application of sericin as a biomaterial. Here, we produce a sericin-like protein (Ser4mer) with native sequence of sericin encoding four repeats of the conserved 38 amino acid motif recombinantly in Escherichia coli and characterize its structural properties. Ser4mer protein shows similar structure to native sericin and higher solubility than previously obtained recombinant sericin-like proteins. Recombinant production of a soluble sericin-like protein will significantly expand its applications as a biomaterial. In addition, recombinant production of silk proteins will allow us to understand sequence-structure relationships in these proteins.