Bioengineering / Biyomühendislik
Permanent URI for this collectionhttps://hdl.handle.net/11147/4529
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Article Citation - WoS: 6Citation - Scopus: 6Microbial Desalination Cell Treated Spent Geothermal Brine as a Nutrient Medium in Hydroponic Lettuce Cultivation: Health Risk Assessment(Elsevier, 2024) Goren, A. Y.; Eskisoy, D. N.; Genisoglu, S.; Okten, H. E.The scarcity and contamination of freshwater resources are extremely critical issues today, and the expansion of water reuse has been considered as an option to decrease its impact. Therefore, the reuse of microbial desalination (MDC)-treated spent geothermal brine for agricultural purposes arises as a good solution to prevent water contamination and provide sustainable water usage. In this study, the potential of treated spent geothermal water from MDC system as a nutrient solution for the hydroponic cultivation of lettuce was evaluated. The effects of different water samples (Hoagland solution (R1) as a control, MDC-treated water (R2), 1:1, v/v mixture of MDCtreated water and Hoagland solution (R3), 4:1, v/v mixture of MDC-treated water and Hoagland solution (R4), and tap water (R5)) on lettuce growth were considered. The application of R3 and R4 samples for hydroponic lettuce cultivation was promising since the lettuce plants uptake sufficient nutrients for their growth and productivity with low toxic metal concentrations. In addition, the chlorophyll-a, chlorophyll-b, and carotene contents of lettuce were in the range of 1.045-2.391 mg/g, 0.761-1.986 mg/g, and 0.296-0.423 mg/g in different water samples, respectively. The content of chlorophyll-a was highest in R1 (2.391 mg/g), followed by R3 (2.371 mg/g). Furthermore, the health risk assessment of heavy metal accumulations in the lettuce plants cultivated in the various water samples was determined. Results showed that heavy metal exposure via lettuce consumption is unlikely to suffer noticeable adverse health problems with values below the permissible limit value.Article Citation - WoS: 4Citation - Scopus: 4Optimizing the Dispersion of Calcium Phosphate Nanoparticles for Cellular Studies Using Statistical Design of Experiments(Elsevier, 2023) Önder, Anıl Can; Tomak, Aysel; Öksel Karakuş, CeydaThe in vitro experimentation of ceramic nanoparticles often requires their dispersion in liquid media without causing particle clumps or deteriorating sample integrity. However, the dispersion of nanoparticles using the available protocols rarely leads to stable and uniform dispersions which, in turn, raises concerns about the validity, repeatability and comparability of the findings observed in vitro. Moreover, the ability to control the final dispersion quality of ceramic nanoparticles is an essential step to obtaining optimized nanoceramic materials with desired functionality and to enhancing their performance in subsequent applications. While the need to have a comprehensive guideline for the dispersion of nanoparticles has led to several published documents and protocols, the dispersion methodology of ceramic nanoparticles and the relative contribution of the experimental parameters to the quality of resulting dispersion are still not clear. Here, we employed the statistical design of experiment (DoE) approach to systematically assess the magnitude and source of variation in dispersion quality of two different ceramic nanoparticles, hydroxyapatite and tricalcium phosphate. Using the first-order Plackett-Burman Design (PBD), nanoparticle concentration, pH and the presence of an additive were identified as the most critical factors influencing the resulting hydrodynamic size and zeta potential of the ceramic nanoparticles. Optimization using a second-order Central Composite Design (CCD) yielded a set of quadratic regression equations that were used to predict the hydrodynamic size or zeta potential of ceramic nanoparticles with high accuracy (R2, 0.88–0.92). The results of PBD screening and CCD optimization experiments were employed to prepare nanoparticle dispersions of different quality, which were then used to compare the effect of aggregation on the viability of human osteosarcoma (SaOS-2) cells. Overall, the results of this study provided insight into the role that various experimental parameters play in the colloidal stability and dispersion of ceramic nanoparticles. © 2023Article Citation - WoS: 19Citation - Scopus: 21Telomerase Activators From 20(27)-Octanor Via Biotransformation by the Fungal Endophytes(Academic Press, 2021) Duman, Seda; Ekiz, Güner; Yılmaz, Sinem; Yusufoğlu, Hasan; Ballar Kırmızıbayrak, Petek; Bedir, ErdalCycloastragenol [20(R),24(S)-epoxy-3 beta,6 alpha,16 beta,25-tetrahydroxycycloartane] (CA), the principle sapogenol of many cycloartane-type glycosides found in Astragalus genus, is currently the only natural product in the anti-aging market as telomerase activator. Here, we report biotransformation of 20(27)-octanor-cycloastragenol (1), a thermal degradation product of CA, using Astragalus species originated endophytic fungi, viz. Penicillium roseopurpureum, Alternaria eureka, Neosartorya hiratsukae and Camarosporium laburnicola. Fifteen new biotransformation products (2-16) were isolated, and their structures were established by NMR and HRESIMS. Endophytic fungi were found to be capable of performing hydroxylation, oxidation, ring cleavage-methyl migration, dehydrogenation and Baeyer-Villiger type oxidation reactions on the starting compound (1), which would be difficult to achieve by conventional synthetic methods. In addition, the ability of the metabolites to increase telomerase activation in Hekn cells was evaluated, which showed from 1.08 to 12.4-fold activation compared to the control cells treated with DMSO. Among the compounds tested, 10, 11 and 12 were found to be the most potent in terms of telomerase activation with 12.40-, 7.89- and 5.43-fold increase, respectively (at 0.1, 2 and 10 nM concentrations, respectively).Article Citation - WoS: 19Citation - Scopus: 21Bacterial Cellulose Based Facial Mask With Antioxidant Property and High Moisturizing Capacity(Springer, 2021) Bilgi, Eyüp; Homan Gökçe, Evren; Bayır, Ece; Şendemir, Aylin; Özgen Özer, Kevser; Hames Tuna, Elif EsinBacterial cellulose (BC) produced by certain bacteria has the potential to be used in many different areas. Despite its advantageous properties compared to plant cellulose, such as high purity, mechanical strength, nanofiber mesh structure, and high-water holding capacity, its production through a biotechnological process prevents it from competing with plant counterparts in terms of cost-effectiveness. Therefore, studies have focused on the development of culture media with cost-effective BC production methods and the production of high value-added products from BC. In this study, it was aimed to develop a taurine-loaded moisturizing facial mask with antioxidant properties based on BC's high-water retention and chemical retention capacity. BC facial mask samples were characterized by Scanning Electron Microscopy (SEM) imaging, Fourier Transform Infrared (FTIR) Spectroscopy, Differential Scanning Calorimetry (DSC), Liquid Chromatography-Mass spectrometry (LC-MS), microbial and mechanical stability tests, as well as cytotoxicity tests. According to our results, produced facial mask samples did not show any cytotoxic effect on human keratinocyte (HS2) or mouse fibroblast (L-929) cell lines; it has high thermal stability, which makes it suitable for different sterilization techniques including sterilization by heat treatment. Taurine release (over 2 mu g/mL in 5 min) and microbial stability tests (no bacterial growth observed) of packaged products kept at 40 and 25 degrees C for 6 months have shown that the product preserves its characteristics for a long time. In conclusion bacterial cellulose-based facial masks are suitable for use as a facial mask, and they can be used for moisturizing and antioxidant properties by means of taurine.Article Citation - WoS: 61Citation - Scopus: 64Electrospun Gelma Fibers and P(hema) Matrix Composite for Corneal Tissue Engineering(Elsevier Ltd., 2021) Arıca, Tuğçe A.; Güzelgülgen, Meltem; Yıldız, Ahu Arslan; Demir, Mustafa MuammerThe 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 Elsevier B.V.Article Citation - WoS: 5Citation - Scopus: 6Boosting Up Printability of Biomacromolecule Based Bio-Ink by Modulation of Hydrogen Bonding Pairs(Elsevier Ltd., 2020) Köksal, Büşra; Önbaş, Rabia; Başkurt, Mehmet; Şahin, Hasan; Arslan Yıldız, Ahu; Yıldız, Ümit HakanThis 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 O[dbnd]CN[sbnd]H. 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. © 2020 Elsevier LtdArticle Citation - WoS: 14Citation - Scopus: 17Biocompatibility of Silicon Nitride Produced Via Partial Sintering & Tape Casting(Elsevier Ltd., 2021) Çeçen, Berivan; Topateş, Gülsüm; Kara, Aylin; Akbulut, Serdar Onat; Havıtçıoğlu, Hasan; Kozacı, Leyla DidemThe biocompatibility of silicon nitride ceramics was proven by several studies however this study is apart from the literature in the manner of production routes that are tape casting and partial sintering. We report the tape casting route was chosen and a porous structure was obtained by partial sintering technique. Tape casting brought a smooth surface to the samples. Density and pore size distribution analysis showed that the scaffolds have low density because of the porous structure. XRD and SEM analyses were carried out to reveal the phase and microstructural characteristics of porous ceramic samples. Static contact angle measurement was done for the characterization of the wettability of the scaffolds. It revealed that the surface of the scaffolds was highly hydrophilic which is a desirable characteristic for the protein and cell adhesion. The mechanical characteristics of the scaffolds were analyzed by compression tests. Human osteosarcoma cells were used for in vitro studies. Cell-proliferation and cytotoxicity were analyzed by WST-1 and LDH, respectively. The osteoblastic behavior of the cells on the surface of the scaffolds was identified by alkaline phosphatase activity. BCA analysis was used for total protein content. The BCA and ALP results showed an increasing trend which is directly correlated with cell proliferation. Cells on the surface of the silicon nitride scaffolds were visualized by SEM and fluorescence microscopy where the images supported the in vitro analysis. Therefore, porous silicon nitride scaffolds fabricated via tape casting and partial sintering were biocompatible and they are possible candidates as bone substitute elements. © 2020 Elsevier Ltd and Techna Group S.r.l.Article Citation - WoS: 34Citation - Scopus: 36Biomimetic Hybrid Scaffold Consisting of Co-Electrospun Collagen and Pllcl for 3d Cell Culture(Elsevier Ltd., 2019) Türker, Esra; Yıldız, Ümit Hakan; Arslan Yıldız, AhuElectrospun 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-epsilon-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. (c) 2019 Elsevier B.V. All rights reserved.Article Citation - WoS: 16Citation - Scopus: 17Antiproliferative Activity of (r)-4 '-methylklavuzon on Hepatocellular Carcinoma Cells and Epcam(+)/Cd133(+) Cancer Stem Cells Via Sirt1 and Exportin-1 (crm1) Inhibition(Elsevier Ltd., 2019) Delman, Murat; Avcı, Sanem Tercan; Akçok, İsmail; Kanbur, Tuğçe; Erdal, Esra; Çağır, AliCytotoxic effects of (R)-4'-methylklavuzon were investigated on hepatocellular carcinoma cells (HuH-7 and HepG2) and HuH-7 EpCAM(+)/CD133(+) cancer stem cells. IC50 of (R)-4'-methylklavuzon was found as 1.25 mu M for HuH-7 parental cells while it was found as 2.50 mu M for HuH-7 EpCAM(+)/CD133(+) cancer stem cells. (R)-4'-methylklavuzon tended to show more efficient in vitro cytotoxicity with its lower IC50 values on hepatocellular carcinoma cell lines compared to its lead molecule, goniothalamin and FDA-approved drugs, sorafenib and regorafenib. Cell-based Sirtuin/HDAC enzyme activity measurements revealed that endogenous Sirtuin/HDAC enzymes were reduced by 40% compared to control. SIRT1 protein levels were upregulated indicating triggered DNA repair mechanism. p53 was overexpressed in HepG2 cells. (R)-4'methylklavuzon inhibited CRM1 protein providing increased retention of p53 and RIOK2 protein in the nucleus. HuH-7 parental and EpCAM(+)/CD133(+) cancer stem cell spheroids lost intact morphology. 3D HepG2 spheroid viabilities were decreased in a correlation with upregulation in p53 protein levels. (C) 2019 Elsevier Masson SAS. All rights reserved.Article Citation - WoS: 23Citation - Scopus: 22Microbial Transformation of Cycloastragenol and Astragenol by Endophytic Fungi Isolated From Astragalus Species(American Chemical Society, 2019) Ekiz, Güner; Yılmaz, Sinem; Yusufoğlu, Hasan; Ballar Kırmızıbayrak, Petek; Bedir, ErdalBiotransformation of Astragalus sapogenins (cycloastragenol (1) and astragenol (2)) by Astragalus species originated endophytic fungi resulted in the production of five new metabolites (3, 7, 10, 12, 14) together with 10 known compounds. The structures of the new compounds were established by NMR spectroscopic and HRMS analysis. Oxygenation, oxidation, epoxidation, dehydrogenation, and ring cleavage reactions were observed on the cycloartane (9,19-cyclolanostane) nucleus. The ability of the compounds to increase telomerase activity in neonatal cells was also evaluated. After prescreening studies to define potent telomerase activators, four compounds were selected for subsequent bioassays. These were performed using very low doses ranging from 0.1 to 30 nM compared to the control cells treated with DMSO. The positive control cycloastragenol and 8 were found to be the most active compounds, with 5.2- (2 nM) and 5.1- (0.5 nM) fold activations versus DMSO, respectively. At the lowest dose of 0.1 nM, compounds 4 and 13 provided 3.5- and 3.8-fold activations, respectively, while cycloastragenol showed a limited activation (1.5-fold).