Bioengineering / Biyomühendislik
Permanent URI for this collectionhttps://hdl.handle.net/11147/4529
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Conference Object Bioethanol Production From Low Cost Agro-Industrial Waste Products(Elsevier, 2012) Evcan, Ezgi; Tarı, Canan; Özen, BanuIn recent years, the rapid increase in environmental problems, greenhouse gas emissions, fuel prices and the unlimited consumption of limited fossil fuel stocks made people search for some alternative energy sources. Bioethanol is one of the most popular alternative source with its many beneficial features. Besides, bioethanol which will be obtained from low cost raw materials will be more attractive. Bioethanol produced from lignocellulosic biomass sources, such as agricultural residues, offers unique environmental and economic benefits.Conference Object In Vitro Antitumor Activity of Sarcopoterium Spinosum Leaf Extract With Bioactive Natural Compounds(Elsevier, 2013) Süngüç, Ceren; Erdoğan, İpek; Uslu, Mehmet Emin; Bayraktar, OğuzCancer cell lines cause generation of reactive oxygen species and free radicals at high levels (Wang and Yi, 2008). Then generated free radicals lead to breakdown of the structure of DNA, lipid or protein (Gul et al., 2011). When plant extracts including antioxidant phytochemicals are exposed to the redox reactions, the harmful effects of free radicals are effectively prevented. The aim of present research was to evaluate the antitumor potential of the extract derived from Sarcopoterium spinosum leaves. The leaves of S. spinosum were collected in Izmir, Turkey. Total phenol content of ethanolic.Conference Object Investigation of Anti-Tumoral Activity of Cistus Creticus Extract Against Pc-3 Cell Line(Elsevier, 2013) Erdoğan, İpek; Süngüç, Ceren; Uslu, Mehmet Emin; Bayraktar, OğuzRecent studies have revealed that plant extracts show cytotoxic activities against cancer cell lines by ceasing cell division in particular phases (Xu et al., 2012, Yıldırım et al., 2013). Expression of specific genes was found to be activated according to pathway in which cell death occurs. Objective of this study was to identify antitumoural effect of Cistus creticus, which is a perennial shrub, found in Mediterranean region, against prostate cancer cell line by measuring the cytotoxic activities and apoptotic gene expression levels.Conference Object Investigation of Antimicrobial Activity To Determine Mic Value of Cinnamon Bark Oil Against Helicobacter Pylori(Wiley, 2014) Güneş, Seda; Becerikli, T.; Tıhmınlıoğlu, Funda; Yılmaz, Özlem[No abstract available]Article Citation - WoS: 33Citation - Scopus: 34Effects of N-Terminal and C-Terminal Polyhistidine Tag on the Stability and Function of the Thermophilic P450 Cyp119(Hindawi Publishing Corporation, 2019) Aslantaş, Yaprak; Sürmeli, Nur BaşakBiocatalysts are sought-after in synthesis of pharmaceuticals and agrochemicals due to their high regioselectivity and enantioselectivity. Among biocatalysts, heme-containing cytochrome P450 (P450) oxygenases are an attractive target since they catalyze oxidation of "unactivated" carbon-hydrogen bonds with high efficiency. CYP119 is an acidothermophilic P450 from Sulfolobus acidocaldarius, which has the potential to be widely used as a biocatalyst since it shows activity at high temperatures and low pH. Polyhistidine tags (His-tags) are widely used to simplify purification of proteins. However, His-tags can cause changes to protein structure and function. Here, we demonstrate the effects of His-tags on CYP119. To this end, the His-tags were cloned at the N-terminus or C-terminus of the CYP119, and His-tagged proteins were expressed and isolated. The thermostability and peroxidase activity of His-tagged CYP119s were tested and compared to wild type CYP119. Results indicated that while addition of His-tags increased the yield and simplified isolation of CYP119, they also influenced the electronic structure of active site and the activity of the protein. We show that N-terminal His-tagged CYP119 has desirable properties and potential to be used in industrial applications, but mechanistic studies using this protein need careful interpretation since the His-tag affects electronic properties of the active site heme iron.Article Citation - WoS: 24Citation - Scopus: 23Polyethers Isolated From the Marine Actinobacterium Streptomyces Cacaoi Inhibit Autophagy and Induce Apoptosis in Cancer Cells(Elsevier, 2019) Khan, Nasar; Yılmaz, Sinem; Aksoy, Semiha; Uzel, Ataç; Tosun, Çiğdem; Ballar Kırmızıbayrak, Petek; Bedir, ErdalPolyether compounds, a large group of biologically active metabolites produced by Streptomyces species have been reported to show a variety of bioactivity such as antibacterial, antifungal, antiparasitic, antiviral, and tumour cell cytotoxicity. Since some of these compounds target cancer stem cells and multi-drug resistant cancer cells, this family of compounds have become of high interest. In this study, three polyether-type metabolites (1-3), one of which was a new natural product (3), were isolated from the marine derived Streptomyces cacaoi via antimicrobial activity-guided fractionation studies. As several polyether compounds with structural similarity such as monensin have been linked with autophagy and cell death, we first assessed the cytotoxicity of these three compounds. Compounds 2 and 3, but not 1, were found to be cytotoxic in several cell lines with a higher potency towards cancer cells. Furthermore, 2 and 3 caused accumulation of both autophagy flux markers LC3-II and p62 along with cleavage of caspase-3, caspase-9 and poly (ADP-ribose) polymerase 1 (PARP-1). Interestingly, prolonged treatment of the compounds caused a dramatic downregulation of the proteins related to autophagasome formation in a dose dependent manner. Our findings provide insights on the molecular mechanisms of the polyether-type polyketides, and signify their potency as chemotherapeutic agents through inhibiting autophagy and inducing apoptosis.Article Citation - WoS: 13Citation - Scopus: 13Single Chain Cationic Polymer Dot as a Fluorescent Probe for Cell Imaging and Selective Determination of Hepatocellular Carcinoma Cells(American Chemical Society, 2019) Özenler, Sezer; Yücel, Müge; Tüncel, Özge; Kaya, Hakan; Özçelik, Serdar; Yıldız, Ümit HakanThis letter describes formation of single chain cationic polymer dots (Pdots) made of poly[1,4-dimethy1-1-(34(2,4,5-trimethylthiophen-3-yl)oxy)propyl)piperazin-1-ium bromide] conjugated polyelectrolyte (CPE). The single chain Pdot formation relies on a simple process which is a rapid nanophase separation between CPE solution of ethylene glycol and water. Pdots show narrow monodisperse size distribution with a 3.6 nm in diameter exhibiting high brightness and excellent colloidal and optical stability. It has been demonstrated that photoluminescent Pdots provide selective nuclear translocation to hepatocellular carcinoma cells as compared to healthy liver cells. The Pdot labeling effectively discriminates cancer cells in the coculture media. Pdots hold great promise as a luminescent probe to diagnose cancer cells in histology and may guide surgeons during operations to precisely separate out cancerous tissue due to augmented fluorescence brightness.Article Citation - WoS: 79Citation - Scopus: 93Magnetic Force-Based Micro Fluidic Techniques for Cellular and Tissue Bioengineering(Frontiers Media S.A., 2018) Yaman, Sena; Anıl İnevi, Müge; Özçivici, Engin; Tekin, Hüseyin CumhurLive cell manipulation is an important biotechnological tool for cellular and tissue level bioengineering applications due to its capacity for guiding cells for separation, isolation, concentration, and patterning. Magnetic force-based cell manipulation methods offer several advantages, such as low adverse effects on cell viability and low interference with the cellular environment. Furthermore, magnetic-based operations can be readily combined with microfluidic principles by precisely allowing control over the spatiotemporal distribution of physical and chemical factors for cell manipulation. In this review, we present recent applications of magnetic force-based cell manipulation in cellular and tissue bioengineering with an emphasis on applications with microfluidic components. Following an introduction of the theoretical background of magnetic manipulation, components of magnetic force-based cell manipulation systems are described. Thereafter, different applications, including separation of certain cell fractions, enrichment of rare cells, and guidance of cells into specific macro- or micro-arrangements to mimic natural cell organization and function, are explained. Finally, we discuss the current challenges and limitations of magnetic cell manipulation technologies in microfluidic devices with an outlook on future developments in the field.Conference Object In Vitro Evaluation of Bioactive Chitosan Microspheres for Eradicating Helicobacter Pylori Biofilm(Wiley, 2016) Güneş, Seda; Arslan, Nur; Demiray Gürbüz, Ebru; Tıhmınlıoğlu, Funda; Yılmaz, ÖzlemCertain H. pylori strains can form biofilm both inside and outside human host to protect itself under environmental stress. Biofilm contributes to development of antimicrobial resistance by some kind of mechanisms like providing a barrier for diffusion and allowing resistance gene expression.Conference Object Determination of Biofilm Formation by Helicobacter Pylori(Wiley, 2016) Arslan, Nur; Güneş, Seda; Demiray Gürbüz, Ebru; Tıhmınlıoğlu, Funda; Yılmaz, ÖzlemBackground : Certain H. pylori strains form biofilm in laboratory experiments and also on the surface of gastric mucosa, suggesting possible reason for eradication failure by increasing resistance to antimicrobial agents and transmission. Aim : To examine the mature biofilm formation by H. pylori NCTC11637 standard strain in different incubation periods for H. pylori biofilm characterization.
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