Journals
2024 |
A. Baran Sözmen Beste Elveren, Duygu Erdogan Bahadır Mezgil Yalın Bastanlar Hakan Yildiz Ahu Arslan-Yildiz U Development of chrono-spectral gold nanoparticle growth based plasmonic biosensor platform Journal Article Biosensor and Bioelectronics: X, 16 , pp. 100439, 2024. Abstract | Links | BibTeX | Tags: Journals @article{sozmen2024development, title = {Development of chrono-spectral gold nanoparticle growth based plasmonic biosensor platform}, author = {A. Baran Sözmen, Beste Elveren, Duygu Erdogan, Bahadır Mezgil, Yalın Bastanlar, U. Hakan Yildiz, Ahu Arslan-Yildiz}, url = {https://www.sciencedirect.com/science/article/pii/S2590137024000037}, doi = {10.1016/j.biosx.2024.100439}, year = {2024}, date = {2024-01-11}, journal = {Biosensor and Bioelectronics: X}, volume = {16}, pages = {100439}, publisher = {Elsevier}, abstract = {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.}, keywords = {Journals}, pubstate = {published}, tppubtype = {article} } 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. |
2023 |
Onbas, Rabia; Arslan-Yildiz, Ahu Biopatterning of 3D Cellular Model by Contactless Magnetic Manipulation for Cardiotoxicity Screening Journal Article Tissue Engineering Part A, 2023. Abstract | Links | BibTeX | Tags: Journals @article{onbas2023biopatterning, title = {Biopatterning of 3D Cellular Model by Contactless Magnetic Manipulation for Cardiotoxicity Screening}, author = {Rabia Onbas and Ahu Arslan-Yildiz}, url = {https://www.liebertpub.com/doi/10.1089/ten.tea.2023.0197}, doi = {10.1089/ten.tea.2023.0197}, year = {2023}, date = {2023-12-15}, journal = {Tissue Engineering Part A}, abstract = {Patterning cells to create three-dimensional (3D) cell culture models by magnetic manipulation is a promising technique, which is rapid, simple, and cost-effective. This study introduces a new biopatterning approach based on magnetic manipulation of cells with a bioink that consists alginate, cells, and magnetic nanoparticles. Plackett-Burman and Box-Behnken experimental design models were used to optimize bioink formulation where NIH-3T3 cells were utilized as a model cell line. The patterning capability was confirmed by light microscopy through 7 days culture time. Then, biopatterned 3D cardiac structures were formed using H9c2 cardiomyocyte cells. Cellular and extracellular components, F-actin and collagen Type I, and cardiac-specific biomarkers, Troponin T and MYH6, of biopatterned 3D cardiac structures were observed successfully. Moreover, Doxorubicin (DOX)-induced cardiotoxicity was investigated for developed 3D model, and IC50 value was calculated as 8.1 μM for biopatterned 3D cardiac structures, which showed higher resistance against DOX-exposure compared to conventional two-dimensional cell culture. Hereby, developed biopatterning methodology proved to be a simple and rapid approach to fabricate 3D cardiac models, especially for drug screening applications.}, keywords = {Journals}, pubstate = {published}, tppubtype = {article} } Patterning cells to create three-dimensional (3D) cell culture models by magnetic manipulation is a promising technique, which is rapid, simple, and cost-effective. This study introduces a new biopatterning approach based on magnetic manipulation of cells with a bioink that consists alginate, cells, and magnetic nanoparticles. Plackett-Burman and Box-Behnken experimental design models were used to optimize bioink formulation where NIH-3T3 cells were utilized as a model cell line. The patterning capability was confirmed by light microscopy through 7 days culture time. Then, biopatterned 3D cardiac structures were formed using H9c2 cardiomyocyte cells. Cellular and extracellular components, F-actin and collagen Type I, and cardiac-specific biomarkers, Troponin T and MYH6, of biopatterned 3D cardiac structures were observed successfully. Moreover, Doxorubicin (DOX)-induced cardiotoxicity was investigated for developed 3D model, and IC50 value was calculated as 8.1 μM for biopatterned 3D cardiac structures, which showed higher resistance against DOX-exposure compared to conventional two-dimensional cell culture. Hereby, developed biopatterning methodology proved to be a simple and rapid approach to fabricate 3D cardiac models, especially for drug screening applications. |
Muge Yucel Rabia Onbas, Ahu Arslan-Yildiz Umit Hakan Yildiz The Soft Nanodots as Fluorescent Probes for Cell Imaging: Analysis of Cell and Spheroid Penetration Behavior of Single Chain Polymer Dots Journal Article Macromolecular Bioscience, 2023, ISSN: 1616-5195. Abstract | Links | BibTeX | Tags: Journals @article{yucel2023soft, title = {The Soft Nanodots as Fluorescent Probes for Cell Imaging: Analysis of Cell and Spheroid Penetration Behavior of Single Chain Polymer Dots}, author = {Muge Yucel, Rabia Onbas, Ahu Arslan-Yildiz, Umit Hakan Yildiz }, url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/mabi.202300402}, doi = {10.1002/mabi.202300402}, issn = {1616-5195}, year = {2023}, date = {2023-12-15}, journal = {Macromolecular Bioscience}, abstract = {This 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.}, keywords = {Journals}, pubstate = {published}, tppubtype = {article} } This 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. |
Ozefe, Fatih; Arslan-Yildiz, Ahu Fabrication and development of a microfluidic paper-based immunosorbent assay platform (μPISA) for colorimetric detection of hepatitis C Journal Article Analyst, 148 (4), pp. 898–905, 2023. Abstract | Links | BibTeX | Tags: Journals @article{ozefe2023fabrication, title = {Fabrication and development of a microfluidic paper-based immunosorbent assay platform (μPISA) for colorimetric detection of hepatitis C}, author = {Fatih Ozefe and Ahu Arslan-Yildiz}, url = {https://pubs.rsc.org/en/content/articlelanding/2023/an/d2an01761j/unauth}, doi = {10.1039/D2AN01761J}, year = {2023}, date = {2023-01-02}, journal = {Analyst}, volume = {148}, number = {4}, pages = {898--905}, abstract = {Paper-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.}, keywords = {Journals}, pubstate = {published}, tppubtype = {article} } Paper-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. |
2022 |
Yildirim, Özüm; Arslan-Yildiz, Ahu Development of a hydrocolloid bio-ink for 3D bioprinting Journal Article Biomaterials Science, 10 (23), pp. 6707–6717, 2022. Abstract | Links | BibTeX | Tags: Journals @article{yildirim2022development, title = {Development of a hydrocolloid bio-ink for 3D bioprinting}, author = {Yildirim, Özüm and Arslan-Yildiz, Ahu}, url = {https://pubs.rsc.org/en/content/articlehtml/2022/bm/d2bm01184k}, doi = {10.1039/D2BM01184K}, year = {2022}, date = {2022-01-01}, journal = {Biomaterials Science}, volume = {10}, number = {23}, pages = {6707--6717}, abstract = {A new generation of bio-inks that are soft, viscous enough, stable in cell culture, and printable at low printing pressures is required in the current state of 3D bioprinting technology. Hydrogels can meet these features and can mimic the microenvironment of soft tissues easily. Hydrocolloids are a group of hydrogels which have a suitable gelling capacity and rheological properties. According to the literature, polysaccharide-based hydrocolloids are used in the food industry, wound healing technologies, and tissue engineering. Quince seed hydrocolloids (QSHs), which consist of mostly glucuronoxylan, can easily be obtained from quince seeds by water extraction. In this study, the use of a QSH as a bio-ink was investigated. The suitability of QSH for the printing process was assessed by rheological, uniformity and pore factor analyses. Appropriate printing parameters were determined and the characterization of the bioprinted QSHs was performed by SEM analysis, water uptake capacity measurement, and protein adsorption assay. The bioprinted QSHs had excellent water uptake capacity and showed suitable protein adsorption behaviour. Analyses of the biocompatibility and cellular viability of bioprinted QSHs were conducted using NIH-3T3 fibroblast cells and the results were found to be high during short and long-term cell culture periods. It was proved that QSH is a highly promising bio-ink for 3D bioprinting and further tissue engineering applications.}, keywords = {Journals}, pubstate = {published}, tppubtype = {article} } A new generation of bio-inks that are soft, viscous enough, stable in cell culture, and printable at low printing pressures is required in the current state of 3D bioprinting technology. Hydrogels can meet these features and can mimic the microenvironment of soft tissues easily. Hydrocolloids are a group of hydrogels which have a suitable gelling capacity and rheological properties. According to the literature, polysaccharide-based hydrocolloids are used in the food industry, wound healing technologies, and tissue engineering. Quince seed hydrocolloids (QSHs), which consist of mostly glucuronoxylan, can easily be obtained from quince seeds by water extraction. In this study, the use of a QSH as a bio-ink was investigated. The suitability of QSH for the printing process was assessed by rheological, uniformity and pore factor analyses. Appropriate printing parameters were determined and the characterization of the bioprinted QSHs was performed by SEM analysis, water uptake capacity measurement, and protein adsorption assay. The bioprinted QSHs had excellent water uptake capacity and showed suitable protein adsorption behaviour. Analyses of the biocompatibility and cellular viability of bioprinted QSHs were conducted using NIH-3T3 fibroblast cells and the results were found to be high during short and long-term cell culture periods. It was proved that QSH is a highly promising bio-ink for 3D bioprinting and further tissue engineering applications. |
Sözmen, A B; Arslan-Yıldız, A Sensitive and rapid protein assay via magnetic levitation Journal Article Biosensors and Bioelectronics: X, 2022. Abstract | Links | BibTeX | Tags: Journals @article{SOZMEN2022100137, title = {Sensitive and rapid protein assay via magnetic levitation}, author = {A.B. Sözmen and A. Arslan-Yıldız}, doi = {https://doi.org/10.1016/j.biosx.2022.100137}, year = {2022}, date = {2022-01-01}, journal = {Biosensors and Bioelectronics: X}, abstract = {Magnetic levitation (MagLev) is a newly emerging methodology for biosensing that provides a density-based analysis, which is highly sensitive and versatile. In this study, a magnetic levitation based sensor platform was used for protein detection; and sensor platform optimization was performed for both sensitivity and resolution. Bovine Serum Albumin (BSA) was used as a model protein and detection of BSA was carried out by antibody functionalized polystyrene microspheres (PSMs). Various sizes of PSMs were examined and their performances were compared by statistical analyses in terms of limit of detection (LOD), sensitivity, and resolution. Quantification of the protein was done based on the magnetic levitation height differences of antibody functionalized PSMs. For optimization of the methodology, varied PSMs were utilized, and standardization of PSM diameter, concentration of the antibody to be functionalized, and PSM dilution rates were carried out. In conclusion, 20 μm PSMs diluted to 0.005% W/V and functionalized with anti-BSA antibody at a concentration of 28 μg/ml were determined to provide the best resolution for BSA detection. A dynamic range of 100 nM to 1 mM was observed with an LOD value of 4.1 ng/ml. This sensing platform promises a novel approach with a diverse application field and it provides rapid, consistent, and reproducible results with high resolution and sensitivity.}, keywords = {Journals}, pubstate = {published}, tppubtype = {article} } Magnetic levitation (MagLev) is a newly emerging methodology for biosensing that provides a density-based analysis, which is highly sensitive and versatile. In this study, a magnetic levitation based sensor platform was used for protein detection; and sensor platform optimization was performed for both sensitivity and resolution. Bovine Serum Albumin (BSA) was used as a model protein and detection of BSA was carried out by antibody functionalized polystyrene microspheres (PSMs). Various sizes of PSMs were examined and their performances were compared by statistical analyses in terms of limit of detection (LOD), sensitivity, and resolution. Quantification of the protein was done based on the magnetic levitation height differences of antibody functionalized PSMs. For optimization of the methodology, varied PSMs were utilized, and standardization of PSM diameter, concentration of the antibody to be functionalized, and PSM dilution rates were carried out. In conclusion, 20 μm PSMs diluted to 0.005% W/V and functionalized with anti-BSA antibody at a concentration of 28 μg/ml were determined to provide the best resolution for BSA detection. A dynamic range of 100 nM to 1 mM was observed with an LOD value of 4.1 ng/ml. This sensing platform promises a novel approach with a diverse application field and it provides rapid, consistent, and reproducible results with high resolution and sensitivity. |
2021 |
Sözmen, Alper Baran; Yildiz, Ahu Arslan Cost-effective and rapid prototyping of PMMA microfluidic device via polymer-assisted bonding Journal Article Microfluidics and Nanofluidics, 25 (66), 2021. Abstract | Links | BibTeX | Tags: Journals @article{sozmen2021cost, title = {Cost-effective and rapid prototyping of PMMA microfluidic device via polymer-assisted bonding}, author = {Alper Baran Sözmen and Ahu Arslan Yildiz}, url = {https://link.springer.com/article/10.1007/s10404-021-02466-3}, doi = {10.1007/s10404-021-02466-3}, year = {2021}, date = {2021-07-05}, journal = {Microfluidics and Nanofluidics}, volume = {25}, number = {66}, abstract = {Microfluidic systems are relatively new technology field with a constant need of novel and practical manufacturing materials and methods. One of the main shortcomings of current methods is the inability to provide rapid bonding, with high bonding strength, and sound microchannel integrity. Herein we propose a novel method of assembly that overcomes the mentioned limitations. Polymer-assisted bonding is a novel, rapid, simple, and inexpensive method where a polymer is solubilized in a solvent and the constituted solution is used as a bonding agent. In this study, we combined this method with utilization of several phase-changing materials (PCMs) as channel-protective agents. Glauber’s salt appeared to be more suitable as a channel-protective agent compared to rest of the salts that have been used in this study. Based on the bonding strength, quality analyses, leakage tests, and SEM imaging, the superior assisting bonding solvent was determined to be dichloromethane with a PMMA concentration of 2.5% (W/V). It showed a bonding strength of 23.794 MPa and a nearly non-visible bonding layer formation of 2.83 µm in width which is proved by SEM imaging. The said combination of PCM, solvent, and polymer concentration also showed success in leakage tests and an application of micro-droplet generator fabrication. The application was carried out to test the applicability of developed prototyping methodology, which resulted in conclusive outcomes as the droplet generator simulation run in COMSOL Multiphysics version 5.1 software. In conclusion, the developed fabrication method promises simple, rapid, and strong bonding with sharp and clear micro-channel engraving.}, keywords = {Journals}, pubstate = {published}, tppubtype = {article} } Microfluidic systems are relatively new technology field with a constant need of novel and practical manufacturing materials and methods. One of the main shortcomings of current methods is the inability to provide rapid bonding, with high bonding strength, and sound microchannel integrity. Herein we propose a novel method of assembly that overcomes the mentioned limitations. Polymer-assisted bonding is a novel, rapid, simple, and inexpensive method where a polymer is solubilized in a solvent and the constituted solution is used as a bonding agent. In this study, we combined this method with utilization of several phase-changing materials (PCMs) as channel-protective agents. Glauber’s salt appeared to be more suitable as a channel-protective agent compared to rest of the salts that have been used in this study. Based on the bonding strength, quality analyses, leakage tests, and SEM imaging, the superior assisting bonding solvent was determined to be dichloromethane with a PMMA concentration of 2.5% (W/V). It showed a bonding strength of 23.794 MPa and a nearly non-visible bonding layer formation of 2.83 µm in width which is proved by SEM imaging. The said combination of PCM, solvent, and polymer concentration also showed success in leakage tests and an application of micro-droplet generator fabrication. The application was carried out to test the applicability of developed prototyping methodology, which resulted in conclusive outcomes as the droplet generator simulation run in COMSOL Multiphysics version 5.1 software. In conclusion, the developed fabrication method promises simple, rapid, and strong bonding with sharp and clear micro-channel engraving. |
Meltem Guzelgulgen Dilce Ozkendir-Inanc, Umit Hakan Yildiz Ahu Arslan-Yildiz Glucuronoxylan-based quince seed hydrogel: A promising scaffold for tissue engineering applications Journal Article International Journal of Biological Macromolecules, 180 , pp. 729–738, 2021. Abstract | Links | BibTeX | Tags: Journals @article{guzelgulgen2021glucuronoxylan, title = {Glucuronoxylan-based quince seed hydrogel: A promising scaffold for tissue engineering applications}, author = {Meltem Guzelgulgen, Dilce Ozkendir-Inanc, Umit Hakan Yildiz, Ahu Arslan-Yildiz}, url = {https://www.sciencedirect.com/science/article/abs/pii/S0141813021006255?via%3Dihub}, doi = {10.1016/j.ijbiomac.2021.03.096}, year = {2021}, date = {2021-03-21}, journal = {International Journal of Biological Macromolecules}, volume = {180}, pages = {729--738}, abstract = {Natural gums and mucilages from plant-derived polysaccharides are potential candidates for a tissue-engineering scaffold by their ability of gelation and biocompatibility. Herein, we utilized Glucuronoxylan-based quince seed hydrogel (QSH) as a scaffold for tissue engineering applications. Optimization of QSH gelation was conducted by varying QSH and crosslinker glutaraldehyde (GTA) concentrations. Structural characterization of QSH was done by Fourier Transform Infrared Spectroscopy (FTIR). Furthermore, morphological and mechanical investigation of QSH was performed by Scanning Electron Microscopy (SEM) and Atomic Force Microscopy (AFM). The protein adsorption test revealed the suitability of QSH for cell attachment. Biocompatibility of QSH was confirmed by culturing NIH-3T3 mouse fibroblast cells on it. Cell viability and proliferation results revealed that optimum parameters for cell viability were 2 mg mL−1 of QSH and 0.03 M GTA. SEM and DAPI staining results indicated the formation of spheroids with a diameter of approximately 300 μm. Furthermore, formation of extracellular matrix (ECM) microenvironment was confirmed with the Collagen Type-I staining. Here, it was demonstrated that the fabricated QSH is a promising scaffold for 3D cell culture and tissue engineering applications provided by its highly porous structure, remarkable swelling capacity and high biocompatibility.}, keywords = {Journals}, pubstate = {published}, tppubtype = {article} } Natural gums and mucilages from plant-derived polysaccharides are potential candidates for a tissue-engineering scaffold by their ability of gelation and biocompatibility. Herein, we utilized Glucuronoxylan-based quince seed hydrogel (QSH) as a scaffold for tissue engineering applications. Optimization of QSH gelation was conducted by varying QSH and crosslinker glutaraldehyde (GTA) concentrations. Structural characterization of QSH was done by Fourier Transform Infrared Spectroscopy (FTIR). Furthermore, morphological and mechanical investigation of QSH was performed by Scanning Electron Microscopy (SEM) and Atomic Force Microscopy (AFM). The protein adsorption test revealed the suitability of QSH for cell attachment. Biocompatibility of QSH was confirmed by culturing NIH-3T3 mouse fibroblast cells on it. Cell viability and proliferation results revealed that optimum parameters for cell viability were 2 mg mL−1 of QSH and 0.03 M GTA. SEM and DAPI staining results indicated the formation of spheroids with a diameter of approximately 300 μm. Furthermore, formation of extracellular matrix (ECM) microenvironment was confirmed with the Collagen Type-I staining. Here, it was demonstrated that the fabricated QSH is a promising scaffold for 3D cell culture and tissue engineering applications provided by its highly porous structure, remarkable swelling capacity and high biocompatibility. |
Onbas, Rabia; Yildiz, Ahu Arslan Fabrication of Tunable 3D Cellular Structures in High Volume Using Magnetic Levitation Guided Assembly Journal Article ACS Applied Bio Materials, 4 (2), pp. 1794–1802, 2021. Abstract | Links | BibTeX | Tags: Journals @article{onbas2021fabrication, title = {Fabrication of Tunable 3D Cellular Structures in High Volume Using Magnetic Levitation Guided Assembly}, author = {Rabia Onbas and Ahu Arslan Yildiz}, url = {https://pubs.acs.org/doi/10.1021/acsabm.0c01523}, doi = {10.1021/acsabm.0c01523}, year = {2021}, date = {2021-01-25}, journal = {ACS Applied Bio Materials}, volume = {4}, number = {2}, pages = {1794--1802}, abstract = {Tunable and reproducible size with high circularity is an important limitation to obtain three-dimensional (3D) cellular structures and spheroids in scaffold free tissue engineering approaches. Here, we present a facile methodology based on magnetic levitation (MagLev) to fabricate 3D cellular structures rapidly and easily in high-volume and low magnetic field. In this study, 3D cellular structures were fabricated using magnetic levitation directed assembly where cells are suspended and selfassembled by contactless magnetic manipulation in the presence of a paramagnetic agent. The effect of cell seeding density, culture time, and paramagnetic agent concentration on the formation of 3D cellular structures was evaluated for NIH/3T3 mouse fibroblast cells. In addition, magnetic levitation guided cellular assembly and 3D tumor spheroid formation was examined for five different cancer cell lines: MCF7 (human epithelial breast adenocarcinoma), MDA-MB-231 (human epithelial breast adenocarcinoma), SHSY5Y (human bone-marrow neuroblastoma), PC-12 (rat adrenal gland pheochromocytoma), and HeLa (human epithelial cervix adenocarcinoma). Moreover, formation of a 3D coculture model was successfully observed by using MDA-MB-231 dsRED and MDA-MB-231 GFP cells. Taken together, these results indicate that the developed MagLev setup provides an easy and efficient way to fabricate 3D cellular structures and may be a feasible alternative to conventional methodologies for cellular/multicellular studies.}, keywords = {Journals}, pubstate = {published}, tppubtype = {article} } Tunable and reproducible size with high circularity is an important limitation to obtain three-dimensional (3D) cellular structures and spheroids in scaffold free tissue engineering approaches. Here, we present a facile methodology based on magnetic levitation (MagLev) to fabricate 3D cellular structures rapidly and easily in high-volume and low magnetic field. In this study, 3D cellular structures were fabricated using magnetic levitation directed assembly where cells are suspended and selfassembled by contactless magnetic manipulation in the presence of a paramagnetic agent. The effect of cell seeding density, culture time, and paramagnetic agent concentration on the formation of 3D cellular structures was evaluated for NIH/3T3 mouse fibroblast cells. In addition, magnetic levitation guided cellular assembly and 3D tumor spheroid formation was examined for five different cancer cell lines: MCF7 (human epithelial breast adenocarcinoma), MDA-MB-231 (human epithelial breast adenocarcinoma), SHSY5Y (human bone-marrow neuroblastoma), PC-12 (rat adrenal gland pheochromocytoma), and HeLa (human epithelial cervix adenocarcinoma). Moreover, formation of a 3D coculture model was successfully observed by using MDA-MB-231 dsRED and MDA-MB-231 GFP cells. Taken together, these results indicate that the developed MagLev setup provides an easy and efficient way to fabricate 3D cellular structures and may be a feasible alternative to conventional methodologies for cellular/multicellular studies. |
Bilginer, Rumeysa ; Ozkendir-Inanc, Dilce ; Yildiz, Umit Hakan ; Arslan-Yildiz, Ahu Biocomposite scaffolds for 3D cell culture: Propolis enriched polyvinyl alcohol nanofibers favoring cell adhesion Journal Article Journal of Applied Polymer Science, 138 (17), pp. 50287, 2021. Abstract | Links | BibTeX | Tags: Journals @article{bilginer2021biocomposite, title = {Biocomposite scaffolds for 3D cell culture: Propolis enriched polyvinyl alcohol nanofibers favoring cell adhesion}, author = {Bilginer, Rumeysa and Ozkendir-Inanc, Dilce and Yildiz, Umit Hakan and Arslan-Yildiz, Ahu}, url = {https://onlinelibrary.wiley.com/doi/full/10.1002/app.50287?casa_token=Zos5p_ikjHMAAAAA%3AYoj85Ck45FSO0lS43g71_BZPX5sxA9GdMElnTPxvdx6RxduVhsVkbzytnIKdYsDAMe4AxDcBEDOqInyq}, doi = { https://doi.org/10.1002/app.50287}, year = {2021}, date = {2021-01-01}, journal = {Journal of Applied Polymer Science}, volume = {138}, number = {17}, pages = {50287}, abstract = {The objective of this work is generation of propolis/polyvinyl alcohol (PVA) scaffold by electrospinning for 3D cell culture. Here, PVA used as co-spinning agent since propolis alone cannot be easily processed by electrospinning methodology. Propolis takes charge in maximizing biological aspect of scaffold to facilitate cell attachment and proliferation. Morphological analysis showed size of the electrospun nanofibers varied between 172–523 nm and 345–687 nm in diameter, for non-crosslinked and crosslinked scaffolds, respectively. Incorporation of propolis resulted in desired surface properties of hybrid matrix, where hybrid scaffolds highly favored protein adsorption. To examine cell compatibility, NIH-3T3 and HeLa cells were seeded on propolis/PVA hybrid scaffold. Results confirmed that integration of propolis supported cell adhesion and cell proliferation. Also, results indicated electrospun propolis/PVA hybrid scaffold provide suitable microenvironment for cell culturing. Therefore, developed hybrid scaffold could be considered as potential candidate for 3D cell culture and tissue engineering.}, keywords = {Journals}, pubstate = {published}, tppubtype = {article} } The objective of this work is generation of propolis/polyvinyl alcohol (PVA) scaffold by electrospinning for 3D cell culture. Here, PVA used as co-spinning agent since propolis alone cannot be easily processed by electrospinning methodology. Propolis takes charge in maximizing biological aspect of scaffold to facilitate cell attachment and proliferation. Morphological analysis showed size of the electrospun nanofibers varied between 172–523 nm and 345–687 nm in diameter, for non-crosslinked and crosslinked scaffolds, respectively. Incorporation of propolis resulted in desired surface properties of hybrid matrix, where hybrid scaffolds highly favored protein adsorption. To examine cell compatibility, NIH-3T3 and HeLa cells were seeded on propolis/PVA hybrid scaffold. Results confirmed that integration of propolis supported cell adhesion and cell proliferation. Also, results indicated electrospun propolis/PVA hybrid scaffold provide suitable microenvironment for cell culturing. Therefore, developed hybrid scaffold could be considered as potential candidate for 3D cell culture and tissue engineering. |
Arica, Tugce A; Guzelgulgen, Meltem ; Yildiz, Ahu Arslan ; Demir, Mustafa M Electrospun GelMA fibers and p (HEMA) matrix composite for corneal tissue engineering Journal Article Materials Science and Engineering: C, 120 , pp. 111720, 2021. Abstract | Links | BibTeX | Tags: Journals @article{arica2021electrospun, title = {Electrospun GelMA fibers and p (HEMA) matrix composite for corneal tissue engineering}, author = {Arica, Tugce A and Guzelgulgen, Meltem and Yildiz, Ahu Arslan and Demir, Mustafa M}, url = {https://www.sciencedirect.com/science/article/pii/S0928493120336390?casa_token=coY_zjzESXYAAAAA:KKv42XVXCoXCqjgjrdRwrD9gaC8Npwpk3zsD1Y-1TZJkEWfKEgdxJ2YA8j5jG_xRCSJNl9CrxyE}, doi = {https://doi.org/10.1016/j.msec.2020.111720}, year = {2021}, date = {2021-01-01}, journal = {Materials Science and Engineering: C}, volume = {120}, pages = {111720}, abstract = {The development of biocompatible and transparent three-dimensional materials is desirable for corneal tissue engineering. Inspired from the cornea structure, gelatin methacryloyl-poly(2-hydroxymethyl methacrylate) (GelMA-p(HEMA)) composite hydrogel was fabricated. GelMA fibers were produced via electrospinning and covered with a thin layer of p(HEMA) in the presence of N,N′-methylenebisacrylamide (MBA) as cross-linker by drop-casting. The structure of resulting GelMA-p(HEMA) composite was characterized by spectrophotometry, microscopy, and swelling studies. Biocompatibility and biological properties of the both p(HEMA) and GelMA-p(HEMA) composite have been investigated by 3D cell culture, red blood cell hemolysis, and protein adsorption studies (i.e., human serum albumin, human immunoglobulin and egg white lysozyme). The optical transmittance of the GelMA-p(HEMA) composite was found to be approximately 70% at 550 nm. The GelMA-p(HEMA) composite was biocompatible with tear fluid proteins and convenient for cell adhesion and growth. Thus, as prepared hydrogel composite may find extensive applications in future for the development of corneal tissue engineering as well as preparation of stroma of the corneal material.}, keywords = {Journals}, pubstate = {published}, tppubtype = {article} } The development of biocompatible and transparent three-dimensional materials is desirable for corneal tissue engineering. Inspired from the cornea structure, gelatin methacryloyl-poly(2-hydroxymethyl methacrylate) (GelMA-p(HEMA)) composite hydrogel was fabricated. GelMA fibers were produced via electrospinning and covered with a thin layer of p(HEMA) in the presence of N,N′-methylenebisacrylamide (MBA) as cross-linker by drop-casting. The structure of resulting GelMA-p(HEMA) composite was characterized by spectrophotometry, microscopy, and swelling studies. Biocompatibility and biological properties of the both p(HEMA) and GelMA-p(HEMA) composite have been investigated by 3D cell culture, red blood cell hemolysis, and protein adsorption studies (i.e., human serum albumin, human immunoglobulin and egg white lysozyme). The optical transmittance of the GelMA-p(HEMA) composite was found to be approximately 70% at 550 nm. The GelMA-p(HEMA) composite was biocompatible with tear fluid proteins and convenient for cell adhesion and growth. Thus, as prepared hydrogel composite may find extensive applications in future for the development of corneal tissue engineering as well as preparation of stroma of the corneal material. |
2020 |
Koksal, Busra ; Onbas, Rabia ; Baskurt, Mehmet ; Sah{i}n, Hasan ; Yildiz, Ahu Arslan ; Yildiz, Umit Hakan Boosting up printability of biomacromolecule based bio-ink by modulation of hydrogen bonding pairs Journal Article European Polymer Journal, 141 , pp. 110070, 2020. Abstract | Links | BibTeX | Tags: Journals @article{koksal2020boosting, title = {Boosting up printability of biomacromolecule based bio-ink by modulation of hydrogen bonding pairs}, author = {Koksal, Busra and Onbas, Rabia and Baskurt, Mehmet and Sah{i}n, Hasan and Yildiz, Ahu Arslan and Yildiz, Umit Hakan}, url = {https://www.sciencedirect.com/science/article/pii/S0014305720317845?casa_token=MI1-Vkat3zgAAAAA:dH8imW9IIbqtZFzGsWkXDohmSTwXO9tqS0sbW17MPj8srlbmqjLiJlsECsaoPOIru92Li2w6EhI}, doi = {https://doi.org/10.1016/j.eurpolymj.2020.110070}, year = {2020}, date = {2020-01-01}, journal = {European Polymer Journal}, volume = {141}, pages = {110070}, abstract = {This study describes low dose UV curable and bioprintable new bioink made of hydrogen bond donor-acceptor adaptor molecule 2-isocyanatoethyl methacrylate (NCO)modified gelatin (NCO-Gel). Our theoretical calculations demonstrate that insertion of 2-isocyanatoethyl methacrylate doubles the interaction energy (500 meV) between gelatin chains providing significant contribution in interchain condensation and self-organization as compared to methacrylic anhydride modified gelatin (GelMA). The NCO-Gel exhibits peak around 1720 cm−1 referring to bidentate hydrogen bonding between H-NCO and its counterpart Odouble bondCNsingle bondH. These strong interchain interactions drive chains to be packed and thereby facilitating UV crosslinking. The NCO-Gel is exhibiting a rapid, 10 s gelation process by the exposure of laser (3 W, 365 nm). The dynamic light scattering characterization also reveals that NCO-Gel has faster sol to gel transition as compared to GelMA depending on the UV curing time. The NCO-Gel was found to be more firm and mechanically strong that provides advantages in molding as well as bioprinting processes. Bioprinted NCO-Gel has shown sharp borders and stable 3D geometry as compared to GelMA ink under 10 s UV curing time. The cell viability tests confirm that NCO-Gel facilitates cell proliferation and supports cell viability. We foresee that NCO-Gel bioink formulation provides a promising opportunity when low dose UV curing and rapid printing are required.}, keywords = {Journals}, pubstate = {published}, tppubtype = {article} } This study describes low dose UV curable and bioprintable new bioink made of hydrogen bond donor-acceptor adaptor molecule 2-isocyanatoethyl methacrylate (NCO)modified gelatin (NCO-Gel). Our theoretical calculations demonstrate that insertion of 2-isocyanatoethyl methacrylate doubles the interaction energy (500 meV) between gelatin chains providing significant contribution in interchain condensation and self-organization as compared to methacrylic anhydride modified gelatin (GelMA). The NCO-Gel exhibits peak around 1720 cm−1 referring to bidentate hydrogen bonding between H-NCO and its counterpart Odouble bondCNsingle bondH. These strong interchain interactions drive chains to be packed and thereby facilitating UV crosslinking. The NCO-Gel is exhibiting a rapid, 10 s gelation process by the exposure of laser (3 W, 365 nm). The dynamic light scattering characterization also reveals that NCO-Gel has faster sol to gel transition as compared to GelMA depending on the UV curing time. The NCO-Gel was found to be more firm and mechanically strong that provides advantages in molding as well as bioprinting processes. Bioprinted NCO-Gel has shown sharp borders and stable 3D geometry as compared to GelMA ink under 10 s UV curing time. The cell viability tests confirm that NCO-Gel facilitates cell proliferation and supports cell viability. We foresee that NCO-Gel bioink formulation provides a promising opportunity when low dose UV curing and rapid printing are required. |
Ozefe, Fatih ; Yildiz, Ahu Arslan Smartphone-assisted Hepatitis C detection assay based on magnetic levitation Journal Article Analyst, 145 (17), pp. 5816–5825, 2020. Abstract | Links | BibTeX | Tags: Journals @article{ozefe2020smartphone, title = {Smartphone-assisted Hepatitis C detection assay based on magnetic levitation}, author = {Ozefe, Fatih and Yildiz, Ahu Arslan}, url = {https://pubs.rsc.org/en/content/articlehtml/2020/an/d0an01111h?casa_token=u6fNm2kf_JEAAAAA:VrjbH6o4LrrDbVEvAmsgMOGeUZeEJe0qNQCYj31sTDoBRE8CKNVmpT2uFR8aYpweDi-MUuQ-zeyMaKQ}, doi = {10.1039/D0AN01111H}, year = {2020}, date = {2020-01-01}, journal = {Analyst}, volume = {145}, number = {17}, pages = {5816--5825}, abstract = {This work describes development of smartphone-assisted magnetic levitation assay for Point-of-Care (PoC) applications. Magnetic levitation is a technique that detects and separates particles based on their density differences in a magnetic field. Observation of the levitated micro-particles is mainly performed by light microscope or additional optical components, which mostly limits applicability of the magnetic levitation technique for PoC diagnostics. In this paper, we demonstrated the capability of the smartphone assisted-magnetic levitation platform for Hepatitis C (HCV) detection assay. This method utilizes microsensor beads (MS beads) that are functionalized with anti-HCV NS3 antibody. First, the magnetic levitation platform was optimized via density marker polyethylene beads (DMB); then HCV NS3 protein was successfully detected based on levitation height differences of MS beads caused by density changes. The capability of the magnetic levitation platform for HCV detection was determined as almost 10-fold sensitive compared to conventional techniques such as enzyme-linked immunosorbent assay (ELISA). The imaging capability and resolution of the setup was improved over previously used configurations, and the developed platform enabled visualization of micro-scale objects only by smartphone assistance. This method requires no power, it is an easy-to-use and cost effective, therefore it could be easily adaptable to varied sensing assays as PoC tool.}, keywords = {Journals}, pubstate = {published}, tppubtype = {article} } This work describes development of smartphone-assisted magnetic levitation assay for Point-of-Care (PoC) applications. Magnetic levitation is a technique that detects and separates particles based on their density differences in a magnetic field. Observation of the levitated micro-particles is mainly performed by light microscope or additional optical components, which mostly limits applicability of the magnetic levitation technique for PoC diagnostics. In this paper, we demonstrated the capability of the smartphone assisted-magnetic levitation platform for Hepatitis C (HCV) detection assay. This method utilizes microsensor beads (MS beads) that are functionalized with anti-HCV NS3 antibody. First, the magnetic levitation platform was optimized via density marker polyethylene beads (DMB); then HCV NS3 protein was successfully detected based on levitation height differences of MS beads caused by density changes. The capability of the magnetic levitation platform for HCV detection was determined as almost 10-fold sensitive compared to conventional techniques such as enzyme-linked immunosorbent assay (ELISA). The imaging capability and resolution of the setup was improved over previously used configurations, and the developed platform enabled visualization of micro-scale objects only by smartphone assistance. This method requires no power, it is an easy-to-use and cost effective, therefore it could be easily adaptable to varied sensing assays as PoC tool. |
Bilginer, Rumeysa ; Yildiz, Ahu Arslan A facile method to fabricate propolis enriched biomimetic PVA architectures by co-electrospinning Journal Article Materials Letters, 276 , pp. 128191, 2020. Abstract | Links | BibTeX | Tags: Journals @article{bilginer2020facile, title = {A facile method to fabricate propolis enriched biomimetic PVA architectures by co-electrospinning}, author = {Bilginer, Rumeysa and Yildiz, Ahu Arslan}, url = {https://www.sciencedirect.com/science/article/abs/pii/S0167577X2030896X?casa_token=nx_SKUEYubIAAAAA:BmFnFHg2vv0n62R1MAnmVhAaZPhGtJjYD4DINqHyMQ9ixCF6mhFZRUNLS_PzrjN5Udopyn7laiU}, doi = {https://doi.org/10.1016/j.matlet.2020.128191}, year = {2020}, date = {2020-01-01}, journal = {Materials Letters}, volume = {276}, pages = {128191}, abstract = {This study depicts easy process of propolis by co-electrospinning without using any toxic agent for biomedical applications. To achieve this, polyvinyl alcohol was utilized as co-spinning agent to fabricate biomimetic Propolis/PVA scaffold. Here, whilst PVA was used as a supportive material to accumulate propolis in scaffold, propolis was employed to enrich biologic aspect of scaffold. This strategy overcomes challenges of propolis processing originated from solubility problems and offers easy processability of propolis in order to use in biomedical applications. Electrospun Propolis/PVA scaffolds were crosslinked with glutaraldehyde and drop-cast model was utilized as a control. Formation of porous, bead-free nanofiber architectures was confirmed through surface morphology analysis, while drop-cast model shows non-porous morphology. Wettability results confirmed both crosslinking and integration of propolis into polyvinyl alcohol scaffold moved contact angle to hydrophobic region. Presence and amount of propolis in hybrid scaffolds were validated via absorbance spectrum results. Bioactivity and biocompatibility of propolis-enriched scaffolds were analyzed through protein adsorption capacity. Obtained findings are evidence that electrospinning methodology offers easy and biosafe process of propolis. Electrospun Propolis/PVA exhibits desired properties and could be potentially utilized as scaffold for tissue engineering or as a wound dressing graft in biomedical field.}, keywords = {Journals}, pubstate = {published}, tppubtype = {article} } This study depicts easy process of propolis by co-electrospinning without using any toxic agent for biomedical applications. To achieve this, polyvinyl alcohol was utilized as co-spinning agent to fabricate biomimetic Propolis/PVA scaffold. Here, whilst PVA was used as a supportive material to accumulate propolis in scaffold, propolis was employed to enrich biologic aspect of scaffold. This strategy overcomes challenges of propolis processing originated from solubility problems and offers easy processability of propolis in order to use in biomedical applications. Electrospun Propolis/PVA scaffolds were crosslinked with glutaraldehyde and drop-cast model was utilized as a control. Formation of porous, bead-free nanofiber architectures was confirmed through surface morphology analysis, while drop-cast model shows non-porous morphology. Wettability results confirmed both crosslinking and integration of propolis into polyvinyl alcohol scaffold moved contact angle to hydrophobic region. Presence and amount of propolis in hybrid scaffolds were validated via absorbance spectrum results. Bioactivity and biocompatibility of propolis-enriched scaffolds were analyzed through protein adsorption capacity. Obtained findings are evidence that electrospinning methodology offers easy and biosafe process of propolis. Electrospun Propolis/PVA exhibits desired properties and could be potentially utilized as scaffold for tissue engineering or as a wound dressing graft in biomedical field. |
2019 |
Turker, Esra ; Yildiz, Umit Hakan ; Yildiz, Ahu Arslan Biomimetic hybrid scaffold consisting of co-electrospun collagen and PLLCL for 3D cell culture Journal Article International journal of biological macromolecules, 139 , pp. 1054–1062, 2019. Abstract | Links | BibTeX | Tags: Journals @article{turker2019biomimetic, title = {Biomimetic hybrid scaffold consisting of co-electrospun collagen and PLLCL for 3D cell culture}, author = {Turker, Esra and Yildiz, Umit Hakan and Yildiz, Ahu Arslan}, url = {https://www.sciencedirect.com/science/article/pii/S0141813019350019?casa_token=6PBbzgf5x0QAAAAA:jGOz56rpF4nW2zcV7-h3hEnkMWNLKsOBvlLF35uOfrW7E9TNsVjJVDuVJx-rBGSc12PWGu_pHUY}, doi = {https://doi.org/10.1016/j.ijbiomac.2019.08.082}, year = {2019}, date = {2019-01-01}, journal = {International journal of biological macromolecules}, volume = {139}, pages = {1054--1062}, abstract = {Electrospun collagen is commonly used as a scaffold in tissue engineering applications since it mimics the content and morphology of native extracellular matrix (ECM) well. This report describes “toxic solvent free” fabrication of electrospun hybrid scaffold consisting of Collagen (Col) and Poly(l-lactide-co-ε-caprolactone) (PLLCL) for three-dimensional (3D) cell culture. Biomimetic hybrid scaffold was fabricated via co-spinning approach where simultaneous electrospinning of PLLCL and Collagen was mediated by polymer sacrificing agent Polyvinylpyrrolidone (PVP). Acidified aqueous solution of PVP was used to solubilize collagen without using toxic solvents for electrospinning, and then PVP was readily removed by rinsing in water. Mechanical characterizations, protein adsorption, as well as biodegradation analysis have been conducted to investigate feasibility of biomimetic hybrid scaffold for 3D cell culture applications. Electrospun biomimetic hybrid scaffold, which has 3D-network structure with 300–450 nm fiber diameters, was found to be maximizing cell adhesion through assisting NIH 3T3 mouse fibroblast cells. 3D cell culture studies confirmed that presence of collagen in biomimetic hybrid scaffold have created a major impact on cell proliferation compared to conventional 2D systems on long-term, also cell viability increased with the increasing amount of collagen.}, keywords = {Journals}, pubstate = {published}, tppubtype = {article} } Electrospun collagen is commonly used as a scaffold in tissue engineering applications since it mimics the content and morphology of native extracellular matrix (ECM) well. This report describes “toxic solvent free” fabrication of electrospun hybrid scaffold consisting of Collagen (Col) and Poly(l-lactide-co-ε-caprolactone) (PLLCL) for three-dimensional (3D) cell culture. Biomimetic hybrid scaffold was fabricated via co-spinning approach where simultaneous electrospinning of PLLCL and Collagen was mediated by polymer sacrificing agent Polyvinylpyrrolidone (PVP). Acidified aqueous solution of PVP was used to solubilize collagen without using toxic solvents for electrospinning, and then PVP was readily removed by rinsing in water. Mechanical characterizations, protein adsorption, as well as biodegradation analysis have been conducted to investigate feasibility of biomimetic hybrid scaffold for 3D cell culture applications. Electrospun biomimetic hybrid scaffold, which has 3D-network structure with 300–450 nm fiber diameters, was found to be maximizing cell adhesion through assisting NIH 3T3 mouse fibroblast cells. 3D cell culture studies confirmed that presence of collagen in biomimetic hybrid scaffold have created a major impact on cell proliferation compared to conventional 2D systems on long-term, also cell viability increased with the increasing amount of collagen. |
Sözmen, Alper Baran ; Yildiz, Ahu Arslan Recent Nano Technological Approaches on Capturing, Isolating, and Identifying Circulating Tumor Cells Journal Article Nanoscale Reports, 2 (2), pp. 10–19, 2019. Abstract | Links | BibTeX | Tags: Journals @article{sozmen2019recent, title = {Recent Nano Technological Approaches on Capturing, Isolating, and Identifying Circulating Tumor Cells}, author = {Sözmen, Alper Baran and Yildiz, Ahu Arslan}, url = {https://www.researchgate.net/profile/Alper-Soezmen/publication/332692486_Recent_Nanotechnological_Approaches_on_Capturing_Isolating_and_Identifying_Circulating_Tumor_Cells/links/5ed8e1ff92851c9c5e7bb438/Recent-Nanotechnological-Approaches-on-Capturing-Isolating-and-Identifying-Circulating-Tumor-Cells.pdf}, doi = {DOI: 10.26524/nr1922}, year = {2019}, date = {2019-01-01}, journal = {Nanoscale Reports}, volume = {2}, number = {2}, pages = {10--19}, abstract = {Nano technological approaches are the latest modality for early stage detection of cancer. The need of rapid, non-invasive, patient specific, and informative techniques in cancer diagnostics lead to the utilization of nanotechnology, microfluidics, and lab-on-a-chip platforms for liquid biopsy, and the developments through these technologies increased the knowledge also for case specific applications. In this review, nanotechnology-based methodologies that are developed in the last decade for cancer diagnostics are investigated and are discussed under four main categories for the purpose of simplification as; Nano chip based, Nano film based, magnetic nanomaterialbased methods, and combinational utilization of multiple methodologies. We suggest a combinational approach on device development with an aim of producing a compact, cost effective, rapid, sensitive, and non-invasive diagnostic device as a conclusion of literature review.}, keywords = {Journals}, pubstate = {published}, tppubtype = {article} } Nano technological approaches are the latest modality for early stage detection of cancer. The need of rapid, non-invasive, patient specific, and informative techniques in cancer diagnostics lead to the utilization of nanotechnology, microfluidics, and lab-on-a-chip platforms for liquid biopsy, and the developments through these technologies increased the knowledge also for case specific applications. In this review, nanotechnology-based methodologies that are developed in the last decade for cancer diagnostics are investigated and are discussed under four main categories for the purpose of simplification as; Nano chip based, Nano film based, magnetic nanomaterialbased methods, and combinational utilization of multiple methodologies. We suggest a combinational approach on device development with an aim of producing a compact, cost effective, rapid, sensitive, and non-invasive diagnostic device as a conclusion of literature review. |
2018 |
Turker, E; Demircak, N; Arslan Yildiz, A Scaffold-free cell culturing in three-dimension using magnetic levitation Journal Article Biomater. Sci, 6 , pp. 1745, 2018. Abstract | Links | BibTeX | Tags: Journals @article{turker2018scaffold, title = {Scaffold-free cell culturing in three-dimension using magnetic levitation}, author = {Turker, E and Demircak, N and Arslan Yildiz, A}, url = {https://pubs.rsc.org/en/content/articlehtml/2018/bm/c8bm00122g}, doi = {10.1039/C8BM00122G }, year = {2018}, date = {2018-01-01}, journal = {Biomater. Sci}, volume = {6}, pages = {1745}, abstract = {Three-dimensional (3D) cell culture has emerged as a pioneering methodology and is increasingly utilized for tissue engineering, 3D bioprinting, cancer model studies and drug development studies. The 3D cell culture methodology provides artificial and functional cellular constructs serving as a modular playground prior to animal model studies, which saves substantial efforts, time and experimental costs. The major drawback of current 3D cell culture methods is their dependency on biocompatible scaffolds, which often require tedious syntheses and fabrication steps. Herein, we report an easy-to-use methodology for the formation of scaffold-free 3D cell culture and cellular assembly via magnetic levitation in the presence of paramagnetic agents. To paramagnetize the cell culture environment, three different Gadolinium(III) chelates were utilized, which led to levitation and assembly of cells at a certain levitation height. The assembly and close interaction of cells at the levitation height where the magnetic force was equilibrated with gravitational force triggered the formation of complex 3D cellular structures. It was shown that Gd(III) chelates provided an optimal levitation that induced intercellular interactions in scaffold-free format without compromising cell viability. NIH 3T3 mouse fibroblasts and HCC827 non-small-cell lung cancer cells were evaluated via the magnetic levitation system, and the formation of 3D cell culture models was validated for both cell lines. Hereby, the developed magnetic levitation system holds promises for complex cellular assemblies and 3D cell culture studies.}, keywords = {Journals}, pubstate = {published}, tppubtype = {article} } Three-dimensional (3D) cell culture has emerged as a pioneering methodology and is increasingly utilized for tissue engineering, 3D bioprinting, cancer model studies and drug development studies. The 3D cell culture methodology provides artificial and functional cellular constructs serving as a modular playground prior to animal model studies, which saves substantial efforts, time and experimental costs. The major drawback of current 3D cell culture methods is their dependency on biocompatible scaffolds, which often require tedious syntheses and fabrication steps. Herein, we report an easy-to-use methodology for the formation of scaffold-free 3D cell culture and cellular assembly via magnetic levitation in the presence of paramagnetic agents. To paramagnetize the cell culture environment, three different Gadolinium(III) chelates were utilized, which led to levitation and assembly of cells at a certain levitation height. The assembly and close interaction of cells at the levitation height where the magnetic force was equilibrated with gravitational force triggered the formation of complex 3D cellular structures. It was shown that Gd(III) chelates provided an optimal levitation that induced intercellular interactions in scaffold-free format without compromising cell viability. NIH 3T3 mouse fibroblasts and HCC827 non-small-cell lung cancer cells were evaluated via the magnetic levitation system, and the formation of 3D cell culture models was validated for both cell lines. Hereby, the developed magnetic levitation system holds promises for complex cellular assemblies and 3D cell culture studies. |
Turker, Esra ; Arslan-Yildiz, Ahu Recent advances in magnetic levitation: a biological approach from diagnostics to tissue engineering Journal Article ACS Biomaterials Science & Engineering, 4 (3), pp. 787–799, 2018. Links | BibTeX | Tags: Journals @article{turker2018recent, title = {Recent advances in magnetic levitation: a biological approach from diagnostics to tissue engineering}, author = {Turker, Esra and Arslan-Yildiz, Ahu}, url = {https://pubs.acs.org/doi/abs/10.1021/acsbiomaterials.7b00700?casa_token=O-ifeFDN7Q4AAAAA:2QgAsJQV_Ry95usNioRVdRqdml9S77k7jcsQrYd4Jl0-qj0gePaUTWencOzPx8FRDxuKScaRfg6x6UGB}, doi = {https://doi.org/10.1021/acsbiomaterials.7b00700}, year = {2018}, date = {2018-01-01}, journal = {ACS Biomaterials Science & Engineering}, volume = {4}, number = {3}, pages = {787--799}, keywords = {Journals}, pubstate = {published}, tppubtype = {article} } |
Elveren, Beste ; Yildiz, Ümit Hakan ; Arslan Yildiz, Ahu Utilization of near ir absorbing gold nanocolloids by green synthesis Journal Article Materials Science Forum, 915 , pp. 213–219, 2018. Abstract | Links | BibTeX | Tags: Journals @article{elveren2018utilization, title = {Utilization of near ir absorbing gold nanocolloids by green synthesis}, author = {Elveren, Beste and Yildiz, Ümit Hakan and Arslan Yildiz, Ahu}, url = {https://www.scientific.net/MSF.915.213}, doi = { https://doi.org/10.4028/www.scientific.net/MSF.915.213}, year = {2018}, date = {2018-01-01}, journal = {Materials Science Forum}, volume = {915}, pages = {213--219}, abstract = {The rapid developments in nanoscience, and its applications on biomedical areas have a large impact on drug delivery, tissue engineering, sensing, and diagnosis. Gold is widely investigated nanomaterial for the last couple of decades, since it has unique surface properties and very low toxicity to biological environment. In this work, we present a novel synthesis of gold nanoparticles (GNPs) exhibiting both visible and near-IR absorbance without agglomeration. The surface of GNPs were analyzed by routine methods and the binding kinetics were investigated by Surface Plasmon Resonance (SPR) Spectroscopy. The unique optical properties of near-IR asorbing GNP colloids hold promise for biological applications.}, keywords = {Journals}, pubstate = {published}, tppubtype = {article} } The rapid developments in nanoscience, and its applications on biomedical areas have a large impact on drug delivery, tissue engineering, sensing, and diagnosis. Gold is widely investigated nanomaterial for the last couple of decades, since it has unique surface properties and very low toxicity to biological environment. In this work, we present a novel synthesis of gold nanoparticles (GNPs) exhibiting both visible and near-IR absorbance without agglomeration. The surface of GNPs were analyzed by routine methods and the binding kinetics were investigated by Surface Plasmon Resonance (SPR) Spectroscopy. The unique optical properties of near-IR asorbing GNP colloids hold promise for biological applications. |
2016 |
Arslan-Yildiz, Ahu ; El Assal, Rami ; Chen, Pu ; Guven, Sinan ; Inci, Fatih ; Demirci, Utkan Towards artificial tissue models: past, present, and future of 3D bioprinting Journal Article Biofabrication, 8 (1), pp. 014103, 2016. Abstract | Links | BibTeX | Tags: Journals @article{arslan2016towards, title = {Towards artificial tissue models: past, present, and future of 3D bioprinting}, author = {Arslan-Yildiz, Ahu and El Assal, Rami and Chen, Pu and Guven, Sinan and Inci, Fatih and Demirci, Utkan}, url = {https://iopscience.iop.org/article/10.1088/1758-5090/8/1/014103/meta}, doi = {https://doi.org/10.1088/1758-5090/8/1/014103}, year = {2016}, date = {2016-01-01}, journal = {Biofabrication}, volume = {8}, number = {1}, pages = {014103}, abstract = {Regenerative medicine and tissue engineering have seen unprecedented growth in the past decade, driving the field of artificial tissue models towards a revolution in future medicine. Major progress has been achieved through the development of innovative biomanufacturing strategies to pattern and assemble cells and extracellular matrix (ECM) in three-dimensions (3D) to create functional tissue constructs. Bioprinting has emerged as a promising 3D biomanufacturing technology, enabling precise control over spatial and temporal distribution of cells and ECM. Bioprinting technology can be used to engineer artificial tissues and organs by producing scaffolds with controlled spatial heterogeneity of physical properties, cellular composition, and ECM organization. This innovative approach is increasingly utilized in biomedicine, and has potential to create artificial functional constructs for drug screening and toxicology research, as well as tissue and organ transplantation. Herein, we review the recent advances in bioprinting technologies and discuss current markets, approaches, and biomedical applications. We also present current challenges and provide future directions for bioprinting research.}, keywords = {Journals}, pubstate = {published}, tppubtype = {article} } Regenerative medicine and tissue engineering have seen unprecedented growth in the past decade, driving the field of artificial tissue models towards a revolution in future medicine. Major progress has been achieved through the development of innovative biomanufacturing strategies to pattern and assemble cells and extracellular matrix (ECM) in three-dimensions (3D) to create functional tissue constructs. Bioprinting has emerged as a promising 3D biomanufacturing technology, enabling precise control over spatial and temporal distribution of cells and ECM. Bioprinting technology can be used to engineer artificial tissues and organs by producing scaffolds with controlled spatial heterogeneity of physical properties, cellular composition, and ECM organization. This innovative approach is increasingly utilized in biomedicine, and has potential to create artificial functional constructs for drug screening and toxicology research, as well as tissue and organ transplantation. Herein, we review the recent advances in bioprinting technologies and discuss current markets, approaches, and biomedical applications. We also present current challenges and provide future directions for bioprinting research. |
2015 |
Durmus, Naside Gozde ; Tekin, Cumhur H; Guven, Sinan ; Sridhar, Kaushik ; Yildiz, Ahu Arslan ; Calibasi, Gizem ; Ghiran, Ionita ; Davis, Ronald W; Steinmetz, Lars M; Demirci, Utkan Magnetic levitation of single cells Journal Article Proceedings of the National Academy of Sciences, 112 (28), pp. E3661–E3668, 2015. Abstract | Links | BibTeX | Tags: Journals @article{durmus2015magnetic, title = {Magnetic levitation of single cells}, author = {Durmus, Naside Gozde and Tekin, H Cumhur and Guven, Sinan and Sridhar, Kaushik and Yildiz, Ahu Arslan and Calibasi, Gizem and Ghiran, Ionita and Davis, Ronald W and Steinmetz, Lars M and Demirci, Utkan}, url = {https://www.pnas.org/doi/abs/10.1073/pnas.1509250112}, doi = {https://doi.org/10.1073/pnas.1509250112}, year = {2015}, date = {2015-01-01}, journal = {Proceedings of the National Academy of Sciences}, volume = {112}, number = {28}, pages = {E3661--E3668}, abstract = {Several cellular events cause permanent or transient changes in inherent magnetic and density properties of cells. Characterizing these changes in cell populations is crucial to understand cellular heterogeneity in cancer, immune response, infectious diseases, drug resistance, and evolution. Although magnetic levitation has previously been used for macroscale objects, its use in life sciences has been hindered by the inability to levitate microscale objects and by the toxicity of metal salts previously applied for levitation. Here, we use magnetic levitation principles for biological characterization and monitoring of cells and cellular events. We demonstrate that each cell type (i.e., cancer, blood, bacteria, and yeast) has a characteristic levitation profile, which we distinguish at an unprecedented resolution of 1 × 10−4 g⋅mL−1. We have identified unique differences in levitation and density blueprints between breast, esophageal, colorectal, and nonsmall cell lung cancer cell lines, as well as heterogeneity within these seemingly homogenous cell populations. Furthermore, we demonstrate that changes in cellular density and levitation profiles can be monitored in real time at single-cell resolution, allowing quantification of heterogeneous temporal responses of each cell to environmental stressors. These data establish density as a powerful biomarker for investigating living systems and their responses. Thereby, our method enables rapid, density-based imaging and profiling of single cells with intriguing applications, such as label-free identification and monitoring of heterogeneous biological changes under various physiological conditions, including antibiotic or cancer treatment in personalized medicine.}, keywords = {Journals}, pubstate = {published}, tppubtype = {article} } Several cellular events cause permanent or transient changes in inherent magnetic and density properties of cells. Characterizing these changes in cell populations is crucial to understand cellular heterogeneity in cancer, immune response, infectious diseases, drug resistance, and evolution. Although magnetic levitation has previously been used for macroscale objects, its use in life sciences has been hindered by the inability to levitate microscale objects and by the toxicity of metal salts previously applied for levitation. Here, we use magnetic levitation principles for biological characterization and monitoring of cells and cellular events. We demonstrate that each cell type (i.e., cancer, blood, bacteria, and yeast) has a characteristic levitation profile, which we distinguish at an unprecedented resolution of 1 × 10−4 g⋅mL−1. We have identified unique differences in levitation and density blueprints between breast, esophageal, colorectal, and nonsmall cell lung cancer cell lines, as well as heterogeneity within these seemingly homogenous cell populations. Furthermore, we demonstrate that changes in cellular density and levitation profiles can be monitored in real time at single-cell resolution, allowing quantification of heterogeneous temporal responses of each cell to environmental stressors. These data establish density as a powerful biomarker for investigating living systems and their responses. Thereby, our method enables rapid, density-based imaging and profiling of single cells with intriguing applications, such as label-free identification and monitoring of heterogeneous biological changes under various physiological conditions, including antibiotic or cancer treatment in personalized medicine. |
2013 |
Yildiz, Ahu Arslan ; Kang, CongBao ; Sinner, Eva-Kathrin Biomimetic membrane platform containing hERG potassium channel and its application to drug screening Journal Article Analyst, 138 (7), pp. 2007–2012, 2013. Abstract | Links | BibTeX | Tags: Journals @article{yildiz2013biomimetic, title = {Biomimetic membrane platform containing hERG potassium channel and its application to drug screening}, author = {Yildiz, Ahu Arslan and Kang, CongBao and Sinner, Eva-Kathrin}, url = {https://pubs.rsc.org/en/content/articlehtml/2013/an/c3an36159d}, doi = {10.1039/C3AN36159D}, year = {2013}, date = {2013-01-01}, journal = {Analyst}, volume = {138}, number = {7}, pages = {2007--2012}, abstract = {The hERG (human ether-à-go-go-related gene) potassium channel has been extensively studied by both academia and industry because of its relation to inherited or drug-induced long QT syndrome (LQTS). Unpredicted hERG and drug interaction affecting channel activity is of main concern for drug discovery. Although there are several methods to test hERG and drug interaction, it is still necessary to develop some efficient and economic ways to probe hERG and drug interactions. To contribute this aim, we have developed a biomimetic lipid membrane platform into which the hERG channel can be folded. Expression and integration of the hERG channel was achieved using a cell-free (CF) expression system. The folding of hERG in the biomimetic membrane system was investigated using Surface Plasmon Enhanced Fluorescence Spectroscopy (SPFS) and Imaging Surface Plasmon Resonance (iSPR). In addition, the hERG channel folded into our biomimetic membrane platform was used for probing the channel and drug interactions through fluorescence polarization (FP) assay. Our results suggest that the biomimetic system employed is capable of detecting the interaction between hERG and different channel blockers at varied concentrations. We believe that our current approach could be applied to other membrane proteins for drug screening or other protein-related interactions.}, keywords = {Journals}, pubstate = {published}, tppubtype = {article} } The hERG (human ether-à-go-go-related gene) potassium channel has been extensively studied by both academia and industry because of its relation to inherited or drug-induced long QT syndrome (LQTS). Unpredicted hERG and drug interaction affecting channel activity is of main concern for drug discovery. Although there are several methods to test hERG and drug interaction, it is still necessary to develop some efficient and economic ways to probe hERG and drug interactions. To contribute this aim, we have developed a biomimetic lipid membrane platform into which the hERG channel can be folded. Expression and integration of the hERG channel was achieved using a cell-free (CF) expression system. The folding of hERG in the biomimetic membrane system was investigated using Surface Plasmon Enhanced Fluorescence Spectroscopy (SPFS) and Imaging Surface Plasmon Resonance (iSPR). In addition, the hERG channel folded into our biomimetic membrane platform was used for probing the channel and drug interactions through fluorescence polarization (FP) assay. Our results suggest that the biomimetic system employed is capable of detecting the interaction between hERG and different channel blockers at varied concentrations. We believe that our current approach could be applied to other membrane proteins for drug screening or other protein-related interactions. |
Yildiz, Ahu Arslan ; Yildiz, Umit Hakan ; Liedberg, Bo ; Sinner, Eva-Kathrin Biomimetic membrane platform: fabrication, characterization and applications Journal Article Colloids and Surfaces B: Biointerfaces, 103 , 2013. Abstract | Links | BibTeX | Tags: Journals @article{yildiz2013biomimeticb, title = {Biomimetic membrane platform: fabrication, characterization and applications}, author = {Yildiz, Ahu Arslan and Yildiz, Umit Hakan and Liedberg, Bo and Sinner, Eva-Kathrin}, doi = {10.1016/j.colsurfb.2012.10.066 }, year = {2013}, date = {2013-01-01}, journal = {Colloids and Surfaces B: Biointerfaces}, volume = {103}, abstract = {A facile method for assembly of biomimetic membranes serving as a platform for expression and insertion of membrane proteins is described. The membrane architecture was constructed in three steps: (i) assembly/printing of α-laminin peptide (P19) spacer on gold to separate solid support from the membrane architecture; (ii) covalent coupling of different lipid anchors to the P19 layer to serve as stabilizers of the inner leaflet during bilayer formation; (iii) lipid vesicle spreading to form a complete bilayer. Two different lipid membrane systems were examined and two different P19 architectures prepared by either self-assembly or μ-contact printing were tested and characterized using contact angle (CA) goniometry, surface plasmon resonance (SPR) spectroscopy and imaging surface plasmon resonance (iSPR). It is shown that surface coverage of cushion layer is significantly improved by μ-contact printing thereby facilitating bilayer formation as compared to self-assembly. To validate applicability of proposed methodology, incorporation of Cytochrome bo3 ubiquinol oxidase (Cyt-bo3) into biomimetic membrane was performed by in vitro expression technique which was further monitored by surface plasmon enhanced fluorescence spectroscopy (SPFS). The results showed that solid supported planar membranes, tethered by α-laminin peptide cushion layer, provide an attractive environment for membrane protein insertion and characterization.}, keywords = {Journals}, pubstate = {published}, tppubtype = {article} } A facile method for assembly of biomimetic membranes serving as a platform for expression and insertion of membrane proteins is described. The membrane architecture was constructed in three steps: (i) assembly/printing of α-laminin peptide (P19) spacer on gold to separate solid support from the membrane architecture; (ii) covalent coupling of different lipid anchors to the P19 layer to serve as stabilizers of the inner leaflet during bilayer formation; (iii) lipid vesicle spreading to form a complete bilayer. Two different lipid membrane systems were examined and two different P19 architectures prepared by either self-assembly or μ-contact printing were tested and characterized using contact angle (CA) goniometry, surface plasmon resonance (SPR) spectroscopy and imaging surface plasmon resonance (iSPR). It is shown that surface coverage of cushion layer is significantly improved by μ-contact printing thereby facilitating bilayer formation as compared to self-assembly. To validate applicability of proposed methodology, incorporation of Cytochrome bo3 ubiquinol oxidase (Cyt-bo3) into biomimetic membrane was performed by in vitro expression technique which was further monitored by surface plasmon enhanced fluorescence spectroscopy (SPFS). The results showed that solid supported planar membranes, tethered by α-laminin peptide cushion layer, provide an attractive environment for membrane protein insertion and characterization. |
2012 |
Yildiz, Ahu Arslan ; Knoll, Wolfgang ; Gennis, Robert B; Sinner, Eva-Kathrin Cell-free synthesis of cytochrome bo3 ubiquinol oxidase in artificial membranes Journal Article Analytical biochemistry, 423 , 2012. Abstract | Links | BibTeX | Tags: Journals @article{yildiz2012cell, title = {Cell-free synthesis of cytochrome bo3 ubiquinol oxidase in artificial membranes}, author = {Yildiz, Ahu Arslan and Knoll, Wolfgang and Gennis, Robert B and Sinner, Eva-Kathrin}, doi = {10.1016/j.ab.2012.01.007 }, year = {2012}, date = {2012-01-01}, journal = {Analytical biochemistry}, volume = {423}, abstract = {The analysis of membrane proteins is notoriously difficult because isolation and detergent-mediated reconstitution often results in compromising the protein structure and function. We introduce a novel strategy of combining a cell-free expression method for synthesis of a protein species coping with one of the most important obstacles in membrane protein research—preserving the structural–functional integrity of a membrane protein species and providing a stable matrix for application of analytical tools to characterize the membrane protein of interest. We address integration and subsequent characterization of the cytochrome bo3 ubiquinol oxidase (Cyt-bo3) from de novo synthesis without the effort of conventional cell culture, isolation, and purification procedures. The experimental output supports our idea of a suitable platform for in vitro protein synthesis and functional integration into a membrane-mimicking structure. We show the compatibility of different concepts of in vitro synthesis toward biosensor applicability by the example of Cyt-bo3 protein expression. Our results obtained from in vitro synthesized proteins displayed similar behavior to proteins isolated from the cellular context. Overall, our approach is suitable for the in vitro expression of “complex” protein species such as Cyt-bo3, which can be reproducible and stably synthesized and preserved in robust, synthetic planar membrane architecture.}, keywords = {Journals}, pubstate = {published}, tppubtype = {article} } The analysis of membrane proteins is notoriously difficult because isolation and detergent-mediated reconstitution often results in compromising the protein structure and function. We introduce a novel strategy of combining a cell-free expression method for synthesis of a protein species coping with one of the most important obstacles in membrane protein research—preserving the structural–functional integrity of a membrane protein species and providing a stable matrix for application of analytical tools to characterize the membrane protein of interest. We address integration and subsequent characterization of the cytochrome bo3 ubiquinol oxidase (Cyt-bo3) from de novo synthesis without the effort of conventional cell culture, isolation, and purification procedures. The experimental output supports our idea of a suitable platform for in vitro protein synthesis and functional integration into a membrane-mimicking structure. We show the compatibility of different concepts of in vitro synthesis toward biosensor applicability by the example of Cyt-bo3 protein expression. Our results obtained from in vitro synthesized proteins displayed similar behavior to proteins isolated from the cellular context. Overall, our approach is suitable for the in vitro expression of “complex” protein species such as Cyt-bo3, which can be reproducible and stably synthesized and preserved in robust, synthetic planar membrane architecture. |
Ng, Hui Qi ; Kim, Young Mee ; Huang, Qiwei ; Gayen, Shovanlal ; Yildiz, Ahu Arslan ; Yoon, Ho Sup ; Sinner, Eva-Kathrin ; Kang, CongBao Purification and structural characterization of the voltage-sensor domain of the hERG potassium channel Journal Article Protein Expression and Purification, 86 , 2012. Abstract | Links | BibTeX | Tags: Journals @article{ng2012purification, title = {Purification and structural characterization of the voltage-sensor domain of the hERG potassium channel}, author = {Ng, Hui Qi and Kim, Young Mee and Huang, Qiwei and Gayen, Shovanlal and Yildiz, Ahu Arslan and Yoon, Ho Sup and Sinner, Eva-Kathrin and Kang, CongBao}, doi = {10.1016/j.pep.2012.09.003}, year = {2012}, date = {2012-01-01}, journal = {Protein Expression and Purification}, volume = {86}, abstract = {The hERG (human ether à go-go related gene) potassium channel is a voltage-gated potassium channel playing important roles in the heart by controlling the rapid delayed rectifier potassium current. The hERG protein contains a voltage-sensor domain (VSD) that is important for sensing voltage changes across the membrane. Mutations in this domain contribute to serious heart diseases. To study the structure of the VSD, it was over-expressed in Escherichia coli and purified into detergent micelles. Lyso-myristoyl phosphatidylglycerol (LMPG) was shown to be a suitable detergent for VSD purification and folding. Secondary structural analysis using circular dichroism (CD) spectroscopy indicated that the purified VSD in LMPG micelles adopted α-helical structures. Purified VSD in LMPG micelles produced dispersed cross-peaks in a 15N-HSQC spectrum. Backbone resonance assignments for residues from transmembrane segments S3 and S4 of VSD also confirmed the presence of α-helical structures in this domain. Our results demonstrated that structure of VSD can be investigated using NMR spectroscopy.}, keywords = {Journals}, pubstate = {published}, tppubtype = {article} } The hERG (human ether à go-go related gene) potassium channel is a voltage-gated potassium channel playing important roles in the heart by controlling the rapid delayed rectifier potassium current. The hERG protein contains a voltage-sensor domain (VSD) that is important for sensing voltage changes across the membrane. Mutations in this domain contribute to serious heart diseases. To study the structure of the VSD, it was over-expressed in Escherichia coli and purified into detergent micelles. Lyso-myristoyl phosphatidylglycerol (LMPG) was shown to be a suitable detergent for VSD purification and folding. Secondary structural analysis using circular dichroism (CD) spectroscopy indicated that the purified VSD in LMPG micelles adopted α-helical structures. Purified VSD in LMPG micelles produced dispersed cross-peaks in a 15N-HSQC spectrum. Backbone resonance assignments for residues from transmembrane segments S3 and S4 of VSD also confirmed the presence of α-helical structures in this domain. Our results demonstrated that structure of VSD can be investigated using NMR spectroscopy. |
2007 |
Arslan, Ahu ; Tuerkarslan, Oezlem ; Tanyeli, Cihangir ; Akhmedov, {.I}dris Mecido{u{g}}lu ; Toppare, Levent Electrochromic properties of a soluble conducting polymer: Poly (1-(4-fluorophenyl)-2, 5-di (thiophen-2-yl)-1H-pyrrole) Journal Article Materials chemistry and physics, 104 , 2007. Abstract | Links | BibTeX | Tags: Journals @article{arslan2007electrochromic, title = {Electrochromic properties of a soluble conducting polymer: Poly (1-(4-fluorophenyl)-2, 5-di (thiophen-2-yl)-1H-pyrrole)}, author = {Arslan, Ahu and Tuerkarslan, Oezlem and Tanyeli, Cihangir and Akhmedov, {.I}dris Mecido{u{g}}lu and Toppare, Levent}, doi = {10.1016/j.matchemphys.2007.03.035}, year = {2007}, date = {2007-01-01}, journal = {Materials chemistry and physics}, volume = {104}, abstract = {1-(4-Fluorophenyl)-2,5-di(thiophen-2-yl)-1H-pyrrole (FPTP) was synthesized and polymerized both chemically and electrochemically. Spectroelectrochemistry experiments reflected a π to π* transition with a band gap energy of 1.94 eV for the polymer. A dual type electrochromic device (ECD) of P(FPTP) and poly(3,4-ethylenedioxythiophene) (PEDOT) was constructed. The device switches between yellow and blue upon application of −0.8 V and +1.1 V, respectively. Optical contrast was calculated as 19.4% whereas switching time was found as 1.4 s at maximum contrast point.}, keywords = {Journals}, pubstate = {published}, tppubtype = {article} } 1-(4-Fluorophenyl)-2,5-di(thiophen-2-yl)-1H-pyrrole (FPTP) was synthesized and polymerized both chemically and electrochemically. Spectroelectrochemistry experiments reflected a π to π* transition with a band gap energy of 1.94 eV for the polymer. A dual type electrochromic device (ECD) of P(FPTP) and poly(3,4-ethylenedioxythiophene) (PEDOT) was constructed. The device switches between yellow and blue upon application of −0.8 V and +1.1 V, respectively. Optical contrast was calculated as 19.4% whereas switching time was found as 1.4 s at maximum contrast point. |
2006 |
Arslan, Ahu ; K{i}ralp, Senem ; Toppare, Levent ; Bozkurt, Ayhan Novel conducting polymer electrolyte biosensor based on poly (1-vinyl imidazole) and poly (acrylic acid) networks Journal Article Langmuir, 22 , 2006. Abstract | Links | BibTeX | Tags: Journals @article{arslan2006novel, title = {Novel conducting polymer electrolyte biosensor based on poly (1-vinyl imidazole) and poly (acrylic acid) networks}, author = {Arslan, Ahu and K{i}ralp, Senem and Toppare, Levent and Bozkurt, Ayhan}, doi = {10.1021/la0530539}, year = {2006}, date = {2006-01-01}, journal = {Langmuir}, volume = {22}, abstract = {Biosensor construction and characterization studies of poly(acrylic acid) (PAA) and poly(1-vinyl imidazole) (PVI) complex systems have been carried out. The biosensors were prepared by mixing PAA with PVI at several stoichiometric ratios, x (molar ratio of the monomer repeat units). The enzyme, invertase, was entrapped in the PAA/PVA interpenetrating polymer networks during complexation. Modifications were made on the PAA/PVI conducting polymer electrolyte matrixes to improve the stability and performance of the polymer electrolyte-based enzyme biosensor. The maximum reaction rate (V-max) and Michaelis-Menten constant (K-m) were investigated for the immobilized invertase. The temperature and pH optimization, operational stability, and shelf life of the polymer electrolyte biosensor were also examined.}, keywords = {Journals}, pubstate = {published}, tppubtype = {article} } Biosensor construction and characterization studies of poly(acrylic acid) (PAA) and poly(1-vinyl imidazole) (PVI) complex systems have been carried out. The biosensors were prepared by mixing PAA with PVI at several stoichiometric ratios, x (molar ratio of the monomer repeat units). The enzyme, invertase, was entrapped in the PAA/PVA interpenetrating polymer networks during complexation. Modifications were made on the PAA/PVI conducting polymer electrolyte matrixes to improve the stability and performance of the polymer electrolyte-based enzyme biosensor. The maximum reaction rate (V-max) and Michaelis-Menten constant (K-m) were investigated for the immobilized invertase. The temperature and pH optimization, operational stability, and shelf life of the polymer electrolyte biosensor were also examined. |
2005 |
Arslan, Ahu ; Kiralp, Senem ; Toppare, Levent ; Yagci, Yusuf Immobilization of tyrosinase in polysiloxane/polypyrrole copolymer matrices Journal Article International journal of biological macromolecules, 35 , 2005. Abstract | Links | BibTeX | Tags: Journals @article{arslan2005immobilization, title = {Immobilization of tyrosinase in polysiloxane/polypyrrole copolymer matrices}, author = {Arslan, Ahu and Kiralp, Senem and Toppare, Levent and Yagci, Yusuf}, doi = {10.1016/j.ijbiomac.2005.01.006}, year = {2005}, date = {2005-01-01}, journal = {International journal of biological macromolecules}, volume = {35}, abstract = {Immobilization of tyrosinase in conducting copolymer matrices of pyrrole functionalized polydimethylsiloxane/polypyrrole (PDMS/PPy) was achieved by electrochemical polymerization. The polysiloxane/polypyrrole/tyrosinase electrode was constructed by the entrapment of enzyme in conducting matrices during electrochemical copolymerization. Maximum reaction rate (V(max)) and Michaelis-Menten constant (K(m)) were investigated for immobilized enzyme. Enzyme electrodes were prepared in two different electrolyte/solvent systems. The effect of supporting electrolytes, p-toluene sulfonic acid and sodium dodecyl sulfate on the enzyme activity and film morphology were determined. Temperature and pH optimization, operational stability and shelf-life of enzyme electrodes were also examined. Phenolic contents of green and black tea were determined by using enzyme electrodes.}, keywords = {Journals}, pubstate = {published}, tppubtype = {article} } Immobilization of tyrosinase in conducting copolymer matrices of pyrrole functionalized polydimethylsiloxane/polypyrrole (PDMS/PPy) was achieved by electrochemical polymerization. The polysiloxane/polypyrrole/tyrosinase electrode was constructed by the entrapment of enzyme in conducting matrices during electrochemical copolymerization. Maximum reaction rate (V(max)) and Michaelis-Menten constant (K(m)) were investigated for immobilized enzyme. Enzyme electrodes were prepared in two different electrolyte/solvent systems. The effect of supporting electrolytes, p-toluene sulfonic acid and sodium dodecyl sulfate on the enzyme activity and film morphology were determined. Temperature and pH optimization, operational stability and shelf-life of enzyme electrodes were also examined. Phenolic contents of green and black tea were determined by using enzyme electrodes. |