Bioengineering / Biyomühendislik
Permanent URI for this collectionhttps://hdl.handle.net/11147/4529
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Article Citation - Scopus: 21Determination of Superoxide Dismutase Activities in Different Cyanobacteria for Scavenging of Reactive Oxygen Species(Taylor and Francis Ltd., 2015) Güneş, Seda; Tamburacı, Sedef; İmamoğlu, Esra; Dalay, Meltem ConkThere is considerable interest in cyanobacteria as sources of antioxidant pigments, antiinflammatory substances, enzymes such as superoxide dismutase (SOD) and vitamins. Antioxidant enzymes have significant role in the removal of reactive oxygen species produced during visible and ultraviolet irradiance stress in cyanobacteria. One of the most ubiquitous protective enzyme is superoxide dismutase (SOD). Most of cyanobacteria are known to have both FeSOD and MnSOD which are associated with photosystem I and II. These enzymes are responsible for scavenging superoxide radicals.Spirulina platensis and Synechococcus nidulans are widely used cyanobacteria as food supplement and cosmetic due to their bioactive compounds. Although the chemical composition of S.platensis has been investigated by many researchers, research on the relationship between protein content and comparison of SOD activity with other cyanobacteria is limited.Among several SOD producing cyanobacteria, the most promising organisms were investigate in terms of SOD activities in this study. The aim of the present work was to investigate and compare the SOD activities of different cyanobacteria including S. platensis, Pseudanabeana sp., S. nidulans and associate with protein contents. SOD activities of these cyanobacteria were determined by xanthine/xanthineoxidase method.Modified Lowry method was used for protein determination. The analysis results showed that the maximum specific SOD activity obtained was 50.4 U/mg from S.nidulans and the minimum specific SOD activity was 18.4 U/mg from Pseudanabeana sp. Total protein amount of S. nidulans, S. platensis, Pseudanabeana sp. was determined as 0.25 mg/ml, 0.27 mg/ml and 0.43 mg/ml respectively. As a result, Synechococcus nidulans was more efficient at scavenging peroxide radicals than Pseudanabeana sp. © 2015, © 2015 Har Krishan Bhalla & Sons.Conference Object Deep Convolutional Neural Networks for Viability Analysis Directly From Cell Holograms Captured Using Lensless Holographic Microscopy(The Chemical and Biological Microsystems Society (CBMS), 2019) Delikoyun, Kerem; Çine, Ersin; Anıl İnevi, Müge; Özçivici, Engin; Özuysal, Mustafa; Tekin, Hüseyin CumhurCell viability analysis is one of the most widely used protocols in the fields of biomedical sciences. Traditional methods are prone to human error and require high-cost and bulky instrumentations. Lensless digital inline holographic microscopy (LDIHM) offers low-cost and high resolution imaging. However, recorded holograms should be digitally reconstructed to obtain real images, which requires intense computational work. We introduce a deep transfer learning-based cell viability classification method that directly processes the hologram without reconstruction. This new model is only trained once and viability of each cell can be predicted from its hologram. © 2019 CBMS-0001.Conference Object Citation - Scopus: 2Magnetic Levitation-Based Protein Detection Using Lensless Digital Inline Holographic Microscopy(The Chemical and Biological Microsystems Society (CBMS), 2019) Yaman, Sena; Delikoyun, Kerem; Tekin, Hüseyin CumhurWe present a portable protein detection platform based on magnetic levitation principle integrated with a lensless imaging system. In the platform, polymer microspheres are used to capture selectively target proteins and magnetic nanoparticle labels. The imaging system monitors the levitation height change of polymer microspheres with respect to the presence of target protein on their surfaces. This system enables the detection of target proteins down to ng/mL levels in a short time. © 2019 CBMS-0001.Article Citation - WoS: 13Citation - Scopus: 15Cytotoxic Tolerance of Healthy and Cancerous Bone Cells To Anti-Microbial Phenolic Compounds Depend on Culture Conditions(Humana Press, 2019) Karadaş, Özge; Meşe, Gülistan; Özçivici, EnginCarnosol and carnosic acid are polyphenolic compounds found in rosemary and sage with known anti-oxidant, anti-inflammatory, and anti-microbial properties. Here, we addressed the potential use of carnosol and carnosic acid for in vitro bone tissue engineering applications, specifically depending on their cytotoxic effects on bone marrow stromal and stem cells, and osteosarcoma cells in monolayer and 3D cultures. Carnosol and carnosic acid displayed a bacteriostatic effect on Gram-positive bacteria, especially on S. aureus. The viability results indicated that bone marrow stromal cells and bone marrow stem cells were more tolerant to the presence of carnosol compared to osteosarcoma cells. 3D culture conditions increased this tolerance further for healthy cells, while not affecting the cytotoxic potential of carnosol for osteosarcoma cells. Carnosic acid was found to be more cytotoxic for all cell types used in the study. Results suggest that phenolic compounds might have potential use as anti-microbial and anti-carcinogenic agents for bone tissue engineering with further optimization for controlled release.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: 21Citation - Scopus: 21Development of Adjuvant Nanocarrier Systems for Seasonal Influenza a (h3n2) Vaccine Based on Astragaloside Vii and Gum Tragacanth (aps)(Elsevier, 2019) Yakuboğulları, Nilgün; Genç, Rukan; Coven, Fethiye; Nalbantsoy, Ayşe; Bedir, ErdalAdjuvants are chemical/biological substances that are used in vaccines to increase the immunogenicity of antigens. A few adjuvants have been developed for use in human vaccines because of their limitations including lack of efficacy, unacceptable local or systemic toxicity, the difficulty of manufacturing, poor stability, and high cost. For that reasons, novel adjuvants/adjuvant systems are under search. Astragaloside VII (AST-VII), isolated from Astragalus trojanus, exhibited significant cellular and humoral immune responses. The polysaccharides (APS) obtained from the roots of Astragalus species have been used in traditional Chinese medicine and possess strong immunomodulatory properties. In the present study, the immunomodulatory effects of a newly developed nanocarrier system (APNS: APS containing carrier) and its AST-VII containing formulation (ANS: AST-VII + APNS), on seasonal influenza A (H3N2) vaccine were investigated. Inactivated H3N2 alone or its combinations with test compounds/formulations were intramuscularly injected into Swiss albino mice. Four weeks after immunization, the immune responses were evaluated in terms of antibody and cytokine responses as well as splenocyte proliferation. APNS demonstrated Th2 mediated response by increasing IgG1 antibody titers, whereas ANS showed response towards Th1/Th2 balance and Th17 by producing of IFN-gamma, IL-17A and IgG2a. Based on these results, we propose that APNS and ANS are good candidates to be utilized in seasonal influenza A vaccines as adjuvants/carrier systems. (C) 2019 Elsevier Ltd. All rights reserved.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: 2Citation - Scopus: 2Transition-Metal Direct C-H Arylation of Thiophene in Aqueous Media Via Potassium Peroxymonosulfate(John Wiley and Sons Inc., 2019) Özenler, Sezer; Kaya, Hakan; Elmacı, Nuran; Yıldız, Ümit HakanThis study covers the use of potassium peroxymonosulfate (PPS) which, is a mild and inexpensive catalyst, for direct coupling of C-H/C-H for water soluble thiophene. The 3-(4-methyl-3 '- thienyloxy)propyltriethylammonium bromide (M1) has been selected as model monomer that reacted PPS in 2.0, 0.20 and 0.020 monomer to PPS ratio. The reaction has been monitored via NMR spectroscopy revealing the monomer consumption and formation of dimers to tetramers as well as completion of reaction within 15 minutes. Resultant product is easily collected without tedious work up steps. The computational calculation has optimized the regularity of the coupling as head to tail, tail to tail, head to tail (HT-TT-HT) for tetramer. The regularity of tetramer which is further satisfied via NMR analysis showing emergence of new peaks at 3.56 and 4.48. The shifts in the UV maximum of reactive species have been monitored by absorbance spectroscopy showing time dependent red shift corresponds to growing from monomer to tetramers. The reaction has self-stopped due to low solubility of moderate condensates (higher than trimer), however further experiments have performed in water-organic mixtures showed great promises to obtain higher condensates.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: 8Citation - Scopus: 11Application of Low Intensity Mechanical Vibrations for Bone Tissue Maintenance and Regeneration(TÜBİTAK, 2016) Ölçüm, Melis; Baskan, Öznur; Karadaş, Özge; Özçivici, EnginPhysical exercise is beneficial for bone tissue health, yet its usage is limited for preventing osteoporosis. Even though natural for the bone tissue from development to homeostasis, mechanical loads present with a multitude of physical parameters, including amplitude, duration, frequency, and distribution. Utilizing the most beneficial parameters of mechanical loads may potentiate a nonpharmaceutical tool for biotechnology to prevent and treat bone loss related to aging, bedrest, sedentary lifestyles, weightlessness, and other diseases. Low intensity vibrations (LIVs) consist of mechanical loads with amplitudes smaller than loads prescribed by habitual activity, with a higher frequency. In this review, literature covering LIV signal application on bone tissue and cellular and molecular level is presented. Studies indicate that LIV signals are safe, anabolic, and anticatabolic for skeletal tissue and are of great significance in regenerative medicine applications.