Bioengineering / Biyomühendislik
Permanent URI for this collectionhttps://hdl.handle.net/11147/4529
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Article Citation - WoS: 1Citation - Scopus: 1The Soft Nanodots as Fluorescent Probes for Cell Imaging: Analysis of Cell and Spheroid Penetration Behavior of Single Chain Polymer Dots(Wiley, 2024) Yücel, Müge; Onbaş, Rabia; Arslan Yıldız, Ahu; Yıldız, Ümit HakanThis study describes the formation, size control, and penetration behavior of polymer nanodots (Pdots) consisting of single or few chain polythiophene-based conjugated polyelectrolytes (CPEs) via nanophase separation between good solvent and poor solvent of CPE. Though the chain singularity may be associated with dilution nanophase separation suggests that molecules of a good solvent create a thermodynamically driven solvation layer surrounding the CPEs and thereby separating the single chains even in their poor solvents. This statement is therefore corroborated with emission intensity/lifetime, particle size, and scattering intensity of polyelectrolyte in good and poor solvents. Regarding the augmented features, Pdots are implemented into cell imaging studies to understand the nuclear penetration and to differentiate the invasive characteristics of breast cancer cells. The python based red, green, blue (RGB) color analysis depicts that Pdots have more nuclear penetration ability in triple negative breast cancer cells due to the different nuclear morphology in shape and composition and Pdots have penetrated cell membrane as well as extracellular matrix in spheroid models. The current Pdot protocol and its utilization in cancer cell imaging are holding great promise for gene/drug delivery to target cancer cells by explicitly achieving the very first priority of nuclear intake. The penetration capability of cationic soft nanodots in to tumor models of breast cancer is demonstrated. The image analysis based on fluorescence intensity variation reveals the characteristics of translocation of nanodots in dense mediums such as tumor models.imageArticle Citation - WoS: 14Citation - Scopus: 14Development of Tissue-Engineered Vascular Grafts From Decellularized Parsley Stems(Royal Society of Chemistry, 2023) Çevik, Merve; Dikici, SerkanCardiovascular diseases are mostly associated with narrowing or blockage of blood vessels, and it is the most common cause of death worldwide. The use of vascular grafts is a promising approach to bypass or replace the blocked vessels for long-term treatment. Although autologous arteries or veins are the most preferred tissue sources for vascular bypass, the limited presence and poor quality of autologous vessels necessitate seeking alternative biomaterials. Recently, synthetic grafts have gained attention as an alternative to autologous grafts. However, the high failure rate of synthetic grafts has been reported primarily due to thrombosis, atherosclerosis, intimal hyperplasia, or infection. Thrombosis, the main reason for failure upon implantation, is associated with damage or absence of endothelial cell lining in the vascular graft's luminal surface. To overcome this, tissue-engineered vascular grafts (TEVGs) have come into prominence. Alongside the well-established scaffold manufacturing techniques, decellularized plant-based constructs have recently gained significant importance and are an emerging field in tissue engineering and regenerative medicine. Accordingly, in this study, we demonstrated the fabrication of tubular scaffolds from decellularized parsley stems and recellularized them with human endothelial cells to be used as a potential TEVG. Our results suggested that the native plant DNA was successfully removed, and soft tubular biomaterials were successfully manufactured via the chemical decellularization of the parsley stems. The decellularized parsley stems showed suitable mechanical and biological properties to be used as a TEVG material, and they provided a suitable environment for the culture of human endothelial cells to attach and create a pseudo endothelium prior to implantation. This study is the first one to demonstrate the potential of the parsley stems to be used as a potential TEVG biomaterial. © 2024 The Royal Society of Chemistry.Article Citation - WoS: 18Citation - Scopus: 17Modifying Pickering Polymerized High Internal Phase Emulsion Morphology by Adjusting Particle Hydrophilicity(Elsevier, 2024) Durgut, Enes; Zhou, Muchu; Dikici, Betuel Aldemir; Foudazi, Reza; Claeyssens, FrederikThis study investigates the use of submicron polymeric particles with varying crosslinking densities as the sole stabilizer for producing Polymerized High Internal Phase Emulsions (PolyHIPE). We establish a direct correlation between the crosslinking density and the hydrophilicity of the polymer particles. The hydrophilicity of these particles significantly influences the morphology and rheology of HIPEs. These differences manifest as various morphological variations in the resulting PolyHIPE templates. It was discovered that by increasing the crosslinker weight percentage in the particles from 0 % to 100 %, PolyHIPEs with semi-open, open, and closed porous structures can be obtained. Furthermore, non-crosslinked particles were observed to dissolve in the continuous phase, acting as macromolecular surfactants that generate small pores akin to surfactant-stabilized structures in PolyHIPE. These findings offer fresh insights into the relationship between particle localization at the interface, HIPE rheology, and the formation of pore throats in Pickering PolyHIPEs, leading to the creation of either closed or open porous networks. Additionally, interfacial rheological results demonstrate that particles synthesized with varying monomer-to-crosslinker ratios exhibit different interfacial elasticities, which are linked to PolyHIPE morphology.Article Citation - WoS: 7Citation - Scopus: 8Bioinspired Multi-Layer Biopolymer-Based Dental Implant Coating for Enhanced Osseointegration(Wiley, 2023) Üzülmez, Betül; Demirsoy, Zeynep; Can, Özge; Gülseren, GulcihanThe major drawbacks of metal-based implants are weak osseointegration and post-operational infections. These limitations restrict the long-term use of implants that may cause severe tissue damage and replacement of the implant. Recent strategies to enhance the osseointegration process require an elaborate fabrication process and suffer from post-operative complications. To address the current challenges taking inspiration from the extracellular matrix (ECM), the current study is designed to establish enhanced osseointegration with lowered risk of infection. Natural biopolymer pectin, peptide amphiphiles, and enzyme-mimicking fullerene moieties are governed to present an ECM-like environment around the implant surfaces. This multifunctional approach promotes osseointegration via inducing biomineralization and osteoblast differentiation. Application of the biopolymer-based composite to the metal surfaces significantly enhances cellular attachment, supports the mineral deposition, and upregulates osteoblast-specific gene expression. In addition to the osteoinductive properties of the constructed layers, the inherent antimicrobial properties of multilayer coating are also used to prevent infection possibility. The reported biopolymer-artificial enzyme composite demonstrates antimicrobial activity against Escherichia coli and Bacillus subtilis as a multifunctional surface coating.Conference Object Investigation of the Cytotoxicity of Bioceramic Nanoparticles on Saos-2 Cells by an Alternative Method(Elsevier Ireland Ltd, 2022) Tomak, Aysel; Önder, A. C.; Öksel Karakuş, CeydaReview Citation - WoS: 23Citation - Scopus: 24Microfluidic-Based Technologies for Diagnosis, Prevention, and Treatment of Covid-19: Recent Advances and Future Directions(Springer, 2023) Tarım, Ergün Alperay; Anıl İnevi, Müge; Özkan, İlayda; Keçili, Seren; Bilgi, Eyüp; Başlar, Muhammet Semih; Özçivici, Engin; Öksel Karakuş, Ceyda; Tekin, Hüseyin CumhurThe COVID-19 pandemic has posed significant challenges to existing healthcare systems around the world. The urgent need for the development of diagnostic and therapeutic strategies for COVID-19 has boomed the demand for new technologies that can improve current healthcare approaches, moving towards more advanced, digitalized, personalized, and patient-oriented systems. Microfluidic-based technologies involve the miniaturization of large-scale devices and laboratory-based procedures, enabling complex chemical and biological operations that are conventionally performed at the macro-scale to be carried out on the microscale or less. The advantages microfluidic systems offer such as rapid, low-cost, accurate, and on-site solutions make these tools extremely useful and effective in the fight against COVID-19. In particular, microfluidic-assisted systems are of great interest in different COVID-19-related domains, varying from direct and indirect detection of COVID-19 infections to drug and vaccine discovery and their targeted delivery. Here, we review recent advances in the use of microfluidic platforms to diagnose, treat or prevent COVID-19. We start by summarizing recent microfluidic-based diagnostic solutions applicable to COVID-19. We then highlight the key roles microfluidics play in developing COVID-19 vaccines and testing how vaccine candidates perform, with a focus on RNA-delivery technologies and nano-carriers. Next, microfluidic-based efforts devoted to assessing the efficacy of potential COVID-19 drugs, either repurposed or new, and their targeted delivery to infected sites are summarized. We conclude by providing future perspectives and research directions that are critical to effectively prevent or respond to future pandemics.Article Citation - WoS: 9Citation - Scopus: 9Fabrication and Development of a Microfluidic Paper-Based Immunosorbent Assay Platform (μpisa) for Colorimetric Detection of Hepatitis C(Royal Society of Chemistry, 2023) Özefe, Fatih; Arslan Yıldız, AhuPaper-based microfluidics is an emerging analysis tool used in various applications, especially in point-of-care (PoC) diagnostic applications, due to its advantages over other types of microfluidic devices in terms of simplicity in both production and operation, cost-effectiveness, rapid response time, low sample consumption, biocompatibility, and ease of disposal. Recently, various techniques have been developed and utilized for the fabrication of paper-based microfluidics, such as photolithography, micro-embossing, wax and PDMS printing, etc. In this study, we offer a fabrication methodology for a microfluidic paper-based immunosorbent assay (μPISA) platform and the detection of Hepatitis C Virus (HCV) was carried out to validate this platform. A laser ablation technique was utilized to form hydrophobic barriers easily and rapidly, which was the major advantage of the developed fabrication methodology. The characterization of the μPISA platform was performed in terms of micro-channel properties using bright-field (BF) microscopy, and surface properties using scanning electron microscopy (SEM). At the same time, sample volume and liquid handling capacity were analyzed quantitatively. Ablation speed (S) and laser power (P) were optimized, and it was shown that one combination (10P60S) provided minimal deviation in micro-channel dimensions and prevented deterioration of hydrophobic barriers. Also, the minimum hydrophobic barrier width, which prevents cross-barrier bleeding, was determined to be 255.92 ± 10.01 μm. Furthermore, colorimetric HCV NS3 detection was implemented to optimize and validate the μPISA platform. Here, HCV NS3 in both PBS and human blood plasma was successfully detected by the naked eye at concentrations as low as 1 ng mL−1 and 10 ng mL−1, respectively. Moreover, the limit of detection (LoD) values for HCV NS3 were acquired as 0.796 ng mL−1 in PBS and 2.203 ng mL−1 in human blood plasma with a turnaround time of 90 min. In comparison with conventional ELISA, highly sensitive and rapid HCV NS3 detection was accomplished colorimetrically on the developed μPISA platform.Article Citation - WoS: 7Citation - Scopus: 7Connexin 32 Overexpression Increases Proliferation, Reduces Gap Junctional Intercellular Communication, Motility and Epithelial-To Transition in Hs578t Breast Cancer Cells(Springer, 2022) Uğur, Deniz; Güngül, Taha Buğra; Yücel, Simge; Özçivici, Engin; Yalçın Özuysal, Özden; Meşe Özçivici, GülistanConnexins (Cx) are primary components of gap junctions that selectively allow molecules to be exchanged between adjacent cells, regulating multiple cellular functions. Along with their channel forming functions, connexins play a variety of roles in different stages of tumorigenesis and their roles in tumor initiation and progression is isoform- and tissue-specific. While Cx26 and Cx43 were downregulated during breast tumorigenesis, Cx32 was accumulated in the cytoplasm of the cells in lymph node metastasis of breast cancers and Cx32 was further upregulated in metastasis. Cx32's effect on cell proliferation, gap junctional communication, hemichannel activity, cellular motility and epithelial-to-mesenchymal transition (EMT) were investigated by overexpressing Cx32 in Hs578T and MCF7 breast cancer cells. Additionally, the expression and localization of Cx26 and Cx43 upon Cx32 overexpression were examined by Western blot and immunostaining experiments, respectively. We observed that MCF7 cells had endogenous Cx32 while Hs578T cells did not and when Cx32 was overexpressed in these cells, it caused a significant increase in the percentages of Hs578T cells at the S phase in addition to increasing their proliferation. Further, while Cx32 overexpression did not induce hemichannel activity in either cell, it decreased gap junctional communication between Hs578T cells. Additionally, Cx32 was mainly observed in the cytoplasm in both cells, where it did not form gap junction plaques but Cx32 overexpression reduced Cx43 levels without affecting Cx26. Moreover, migration and invasion potentials of Hs578T and migration in MCF7 were reduced upon Cx32 overexpression. Finally, the protein level of mesenchymal marker N-cadherin decreased while epithelial marker ZO-1 and E-cadherin increased in Hs578T cells. We observed that Cx32 overexpression altered cell proliferation, communication, migration and EMT in Hs578T, suggesting a tumor suppressor role in these cells while it had minor effects on MCF7 cells.Conference Object Citation - WoS: 1Immunomodulatory Mechanisms of Astragalus Saponins(Wiley, 2021) Yakuboğulları, Nilgün; Çağır, Ali; Bedir, Erdal; Sağ, DuyguArticle Citation - WoS: 17Citation - Scopus: 22Protein Corona Formation on Silver Nanoparticles Under Different Conditions(Elsevier, 2022) Tomak, Aysel; Yılancıoğlu, Buket; Winkler, David; Öksel Karakuş, CeydaThe surfaces of nanoparticles become covered by biomolecules in biological fluids. This protein ‘corona’ modifies materials’ characteristics and biological activity. The composition of the protein corona is dynamic, abundant biomolecules that bind first are subsequently replaced by less abundant but more tightly bound ones. Here, we explore the formation of the silver nanoparticle protein corona on exposure to cell culture media containing 10 % fetal bovine serum supplemented Dulbecco's Modified Eagle's medium. Sodium dodecyl-sulfate polyacrylamide gel electrophoresis and liquid chromatography-mass spectrometry/mass spectrometry analysis were used to monitor how different parameters such as incubation time, heating duration, cell culture medium, incubation temperature, and the number of washes affect the nanoparticle–protein corona complex. silver nanoparticles with and without bound proteins were characterized by electron microscopy, dynamic light scattering, and ultraviolet-visible-near-IR spectroscopy. The tetrazolium-based MTT assay was used to determine viability of A549 human lung adenocarcinoma cells treated with silver nanoparticles. Characterization of the nanoparticles before and after protein binding provided insights into their changing morphology on corona formation. Our results confirmed that the physiological environment directly affects protein corona formation on nanoparticle surfaces. In particular, incubation condition-dependent differences in the amount of bound proteins were observed. This work highlights the importance of environmental drivers of protein adsorption, which should be considered when predicting and/or controlling protein targets of silver nanoparticles.
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