Bioengineering / Biyomühendislik
Permanent URI for this collectionhttps://hdl.handle.net/11147/4529
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Article Citation - WoS: 4Citation - Scopus: 5Antioxidant and Antimicrobial Activities of Plants Grown in the Mediterranean Region(John Wiley and Sons Inc., 2022) Kaçar, D.; Bayraktar, Oğuz; Erdem, C.; Alamri, A.S.; Galanakis, C.M.Background: The main objective of this research was to identify plant species with possible bioactivities based on their total phenol content, antioxidant, and antimicrobial properties. Therefore, different parts of 42 plant species grown in the Mediterranean region were extracted with aqueous ethanol solutions to prepare extracts with antioxidant and antimicrobial activities, mainly resulting from their total phenol contents. No detailed laboratory data on the flora of this area exists regarding their total phenol contents and total antioxidant activities. Results: Yields of extraction for each plant material were determined. Extracts were characterized based on their total phenol contents, total antioxidant (both hydrophilic and lipophilic), and antimicrobial activities using Folin–Ciocalteu, Photochemiluminescence, disc diffusion, and microdilution methods, respectively. The extract of Hypericum empetrifolium had the relatively highest total water-soluble and lipid-soluble antioxidant activities. Sarcopoterium spinosum extract had relatively high total phenol content. Preliminary screening study was conducted with the disc diffusion method to evaluate the extracts' antimicrobial activities. 26 out of 42 plant species showed significant antimicrobial activities against the growth of microorganisms. Microdilution assays were performed to evaluate the most active plant species with their minimum inhibition concentrations. H. empetrifolium, Pistacia terebinthus, Arbutus unedo, and Cistus parviflorus were the most antimicrobial plant species among those investigated. CONCLUSION: The new potential sources for the isolation of bioactive natural compounds from specific plant species could be possible with the help of this present screening study. Isolated bioactive natural compounds can be utilized as raw materials in cosmetics, nutraceuticals, food supplements, and pharmaceutical industries. © 2022 Society of Chemical Industry.Article Anthraquinones and Macrocyclic Lactones From Endophytic Fungus Penicillium Roseopurpureum and Their Bioactivities(ACG Publications, 2024) Dizmen,B.; Üner,G.; Küçüksolak,M.; Gören,A.C.; Kırmızıbayrak,P.B.; Bedir,E.Endophytic fungi colonize the internal and distinct tissues of the host plants. In recent years, there has been growing interest in endophytic fungi as valuable sources for drug discovery based on their rich metabolic profiles consisting of novel and bioactive compounds. Accordingly, our preliminary study demonstrated that an endophyte, namely Penicillium roseopurpureum isolated from Astragalus angustifolius, had high chemical diversity with an antiproliferative effect. Herein, fermentation of P. roseopurpureum resulted in the production of five new anthraquinone-type compounds (2, 4, 6, 7, 8) together with several known compounds [11-methoxycurvularin (1: epimeric mixture of 1a and 1b), carviolin (3), 11-hydroxycurvularin (5: diastereoisomeric mixture of 5a and 5b) and 1-O-methylemodin (9)]. The structures of the new compounds were established by NMR spectroscopy and HR-MS analysis. Cytotoxicity studies demonstrated that none of the compounds except for 1 and 5 had antiproliferative activity against prostate cancer cell lines. Interestingly, 1 was found as cytotoxic, whereas 5 exhibited cytostatic properties. Also, 7-AAD/Annexin V staining supported these results by showing that 1 caused cellular death, while 5 did not show any increase in dead cell content in comparison to the control. Lastly, cell cycle analysis showed that compounds had distinctive cell cycle arrest patterns. © 2024 ACG Publications.Article Citation - WoS: 7Citation - Scopus: 8Ascorbic Acid Enhances the Metabolic Activity, Growth and Collagen Production of Human Dermal Fibroblasts Growing in Three-Dimensional (3D) Culture(Gazi Üniversitesi, 2023) Dikici, SerkanTissue engineering (TE) enables the development of functional synthetic substitutes to be replaced with damaged tissues and organs instead of the use of auto or allografts. A wide range of biomaterials is currently in use as TE scaffolds. Among these materials, naturally sourced ones are favorable due to being highly biocompatible and supporting cell growth and function, whereas synthetic ones are advantageous because of the high tunability on mechanical and physical properties as well as being easy to process. Alongside the advantages of synthetic polymers, they mostly show hydrophobic behavior that limits biomaterial-cell interaction and, consequently, the functioning of the developed TE constructs. In this study, we assessed the impact of L-Ascorbic acid 2-phosphate (AA2P) on improving the culture conditions of human dermal fibroblasts (HDFs) growing on a three-dimensional (3D) scaffold made of polycaprolactone (PCL) using emulsion templating. Our results demonstrated that AA2P enhances the metabolic activity and growth of HDFs as well as collagen deposition by them when supplemented in their growth medium at 50 µg/mL concentration. It showed a great potential to be used as a growth medium supplement to circumvent the disadvantages of culturing human cells on a synthetic biomaterial that is not favored in default. AA2P's potential to improve cell growth and collagen deposition may prove an effective way to culture human cells on 3D PCL PolyHIPE scaffolds for various TE applications.Conference Object Biopatterning of 3d Cellular Structures Via Contactless Magnetic Manipulation for Drug Screening(Mary Ann Liebert, 2023) Önbaş, Rabia; Arslan Yıldız, Ahu"Patterning and manipulation techniques have been used to fabricate 3D cell cultures in tissue engineering. The contactless magnetic manipulation approach is a rapid, simple, and cost-effective method that requires paramagnetic agents [1-3] or magnetic materials [4]. Here, to obtain patterned 3D cellular structures a new alginate-based bio-ink formulation was developed to fabricate 3D cellular structures using contactless magnetic manipulation. 3D cardiac model was obtained by patterning rat cardiomyocytes. Cellular and extracellular components and cardiac-specific markers of patterned 3D cellular structures were indicated successfully. Drug response of patterned 3D cellular structures was evaluated by applying doxorubicin. Patterned 3D cardiac cellular structures showed significantly different drug response compared to conventional 2D cell cultures. In conclusion, this technique provides an easy, efficient, and low-cost methodology to fabricate 3D cardiac structures for drug screening.Article Citation - WoS: 6Citation - Scopus: 6Diagnosis of Ruminant Viral Diseases With Loop-Mediated Isothermal Amplification(Springer, 2023) Ayaz Kök, Sanem; Üstün, Selcen; Taşkent, HümeyraInfectious diseases in livestock industry are major problems for animal health, food safety, and the economy. Zoonotic diseases from farm animals are significant threat to human population as well. These are notifiable diseases listed by the World Organization for Animal Health (OIE). Rapid diagnostic methods can help keep infectious diseases under control in herds. Loop-mediated isothermal amplification (LAMP) is a simple and rapid nucleic acid amplification method that is studied widely for detection of many infectious diseases in the field. LAMP allows biosensing of target DNA or RNA under isothermal conditions with high specificity in a short period of time. An untrained user can analyze results based on color change or turbidity. Here we review LAMP assays to diagnose OIE notifiable ruminant viral diseases in literature highlighting properties of LAMP method considering what is expected from an efficient, field usable diagnostic test.Article Citation - WoS: 1Citation - Scopus: 1Expression Profile of Prostaglandin Enzymes in Cystic Endometrial Hyperplasia in Dogs: the Results of a Hypothesis in Clinical Trial(Kafkas Üniversitesi, 2023) Korlu, Yeşim; Yavaş, Özkan; Aktar, Ahmet; Bozkurt, Berkay; Özyiğit, Musa Özgür; Özalp, Gözde RabiaThe expressions of prostaglandin synthesis enzymes and estrogen, progesterone receptors in canine cystic endometrial hyperplasia (CEH) were reported in this manuscript. Uterine tissue samples were collected from bitches with CEH (n=5), CEH-P (Cystic endometrial hyperplasia-Pyometra) (n=5) and healthy-negative control group, CG (n=5). Immunohistochemistry was carried out for the estrogen (ER) and progesterone receptor (PR) detection. Shock-frozen samples were utilized in mRNA extraction and Real-Time PCR was performed. Gene expression of PTGS2/COX2, PTGES, PTGER4, PGFS, PTGFR and PGR were detected higher in the CEH group compared with CG. The PGFS and PTGFR (FP) mRNA expressions were significantly increased in CEH compared with other groups. Expression of progesterone receptor mRNA (PGR) was highest in CEH and statistically different from the CEH-P group (P<0.05). No PR immunostaining was observed. ER staining had been detected in endometrial glands, endometrial stoma and myometrium, however hyperplasic glands in propria mucosa had lower or no ER scores. Based on the results of this study, the high levels of prostaglandin enzymes and low ER scores in CEH could be a preliminary step for the next stages of severe differentiation of endometrium.Article Citation - WoS: 7Citation - Scopus: 7Neo-Clerodanes From Teucrium Divaricatum Subsp. Divaricatum and Their Biological Activity Assessment(Elsevier, 2023) Aydoğan, Fadime; Ali, Zülfiqar; Zülfiqar, Fazila; Karaalp, Canan; Khan, Ikhlas A.; Bedir, ErdalFifteen neo-clerodane diterpenoids (1–15), including two undescribed glycosides, teudivaricosides A (1) and B (2), together with a known iridoid glycoside (16) and a phenylpropanoid glycoside (17) from the whole plant of Teucrium divaricatum subsp. divaricatum were isolated. Their structures were determined by spectral data analysis including 1D and 2D NMR and HRESIMS. Neo-clerodane diterpenoids were evaluated for their anti-inflammatory, and antimicrobial activities. None of them showed significant antimicrobial activity against various bacterial and fungal strains (up to 20 µg/mL). All tested compounds were inactive up to the highest tested concentration of 50 µM on iNOS inhibitory activity.Article Citation - WoS: 3Citation - Scopus: 3Structural and Functional Analyses of Gh51 Alpha-L of Geobacillus Vulcani Gs90 Reveal Crucial Residues for Catalytic Activity and Thermostability(Wiley, 2022) Sürmeli, Yusuf; Şanlı Mohamed, GülşahAlpha-L-arabinofuranosidase (Abf) is of big interest in various industrial areas. Directed evolution is a powerful strategy to identify significant residues underlying Abf properties. Here, six active variants from GH51 Abf of Geobacillus vulcani GS90 (GvAbf) by directed evolution were overproduced, extracted, and analyzed at biochemical and structural levels. According to the activity and thermostability results, the most-active and the least-active variants were found as GvAbf51 and GvAbf52, respectively. GvAbf63 variant was more active than parent GvAbf by 20% and less active than GvAbf51. Also, the highest thermostability belonged to GvAbf52 with 80% residual activity after 1 h. Comparative sequence and structure analyses revealed that GvAbf51 possessed L307S displacement. Thus, this study suggested that L307 residue may be critical for GvAbf activity. GvAbf63 had H30D, Q90H, and L307S displacements, and H30 was covalently bound to E29 catalytic residue. Thus, H30D may decrease the positive effect of L307S on GvAbf63 activity, preventing E29 action. Besides, GvAbf52 possessed S215N, L307S, H473P, and G476C substitutions and S215 was close to E175 (acid–base residue). S215N may partially disrupt E175 action. Overall effect of all substitutions in GvAbf52 may result in the formation of the C–C bond between C171 and C213 by becoming closer to each other.Article Citation - WoS: 25Citation - Scopus: 30Fabrication of 3d Printed Poly(lactic Acid) Strut and Wet-Electrospun Cellulose Nano Fiber Reinforced Chitosan-Collagen Hydrogel Composite Scaffolds for Meniscus Tissue Engineering(SAGE Publications, 2022) Güneş, Oylum Çolpankan; Kara, Aylin; Baysan, Gizem; Hüsemoğlu, Reşit Buğra; Akokay, Pınar; Ziylan Albayrak, Aylin; Ergür, Bekir Uğur; Havitçioğlu, HasanThe main goal of the study was to produce chitosan-collagen hydrogel composite scaffolds consisting of 3D printed poly(lactic acid) (PLA) strut and nanofibrous cellulose for meniscus cartilage tissue engineering. For this purpose, first PLA strut containing microchannels was incorporated into cellulose nanofibers and then they were embedded into chitosan-collagen matrix to obtain micro- and nano-sized topographical features for better cellular activities as well as mechanical properties. All the hydrogel composite scaffolds produced by using three different concentrations of genipin (0.1, 0.3, and 0.5%) had an interconnected microporous structure with a swelling ratio of about 400% and water content values between 77 and 83% which is similar to native cartilage extracellular matrix. The compressive strength of all the hydrogel composite scaffolds was found to be similar (∼32 kPa) and suitable for cartilage tissue engineering applications. Besides, the hydrogel composite scaffold comprising 0.3% (w/v) genipin had the highest tan δ value (0.044) at a frequency of 1 Hz which is around the walking frequency of a person. According to the in vitro analysis, this hydrogel composite scaffold did not show any cytotoxic effect on the rabbit mesenchymal stem cells and enabled cells to attach, proliferate and also migrate through the inner area of the scaffold. In conclusion, the produced hydrogel composite scaffold holds great promise for meniscus tissue engineering.Conference Object On-Chip 3d Cell Culture Platform for Tumor Modeling and Drug Screening(Mary Ann Liebert, 2022) Yıldırım, Özüm; Arslan Yıldız, AhuThree-dimensional (3D) cell culture allows cell-cell and cellmatrix interactions and provides more in vivo like models rather than 2D cell culture which cannot fully mimic native tissue. 3D cell culture on microfluidics allows formation of 3D structures that mimic the physiological and chemical microenvironment for cells[1]. These microfluidic platforms also downsize bench-top laboratory to a microchip, require miniaturized reagent, and are convenient for dynamic drug screening[2]. In this study, a microfluidic platform was designed which is housing a PLLCL scaffold fabricated by electrospinning methodology.