Molecular Biology and Genetics / Moleküler Biyoloji ve Genetik
Permanent URI for this collectionhttps://hdl.handle.net/11147/9
Browse
10 results
Search Results
Article Citation - WoS: 27Citation - Scopus: 30Antibiotic-Resistant Staphylococcus Aureus Does Not Develop Resistance To Vanillic Acid and 2-Hydroxycinnamic Acid After Continuous Exposure in Vitro(American Chemical Society, 2019) Keman, Deniz; Soyer, FerdaDevelopment of resistance to antibiotics is one of the major reasons of difficulties in treatments of diseases caused by antibiotic-resistant bacteria, and this resistance makes the investigation of alternative antimicrobials a key priority. Phenolic acids are plant- and fungi-originating natural antimicrobial products, and there is no known bacterial resistance after exposure to them. The purpose of this study was to investigate the resistance ability of bacteria against phenolic acids. Therefore, the ability of methicillin-resistant Staphylococcus aureus and methicillin-susceptible S. aureus to gain resistance against two phenolic acids and an antibiotic upon exposure to subinhibitory concentrations was tested. Herein, we evaluated the minimum inhibitory concentrations (MICs) of vanillic acid (VA), 2-hydroxycinnamic acid (2-HCA), and vancomycin in the beginning of the experiment and the MICs were found to be 2.5 mg/mL VA, 1.6 mg/mL 2-HCA, and 0.01 mg/mL vancomycin for both bacteria. Following continuous treatments with increasing subinhibitory concentrations, MICs were evaluated once more. Exposure to subinhibitory concentrations of vancomycin induced the development of resistance immediately; however, resistance to both phenolic acids could not be induced. These data indicated the potential of phenolic acids to be used as effective antimicrobials in the inhibition of antibiotic-resistant pathogenic bacteria.Article Citation - WoS: 36Citation - Scopus: 38Effect of Molecular Architecture on Cell Interactions and Stealth Properties of Peg(American Chemical Society, 2017) Özer, İmran; Tomak, Aysel; Zareie, Hadi M.; Baran, Yusuf; Bulmuş, VolgaPEGylation, covalent attachment of PEG to therapeutic biomolecules, in which suboptimal pharmacokinetic profiles limiting their therapeutic utility are of concern, is a widely applied technology. However, this technology has been challenged by reduced bioactivity of biomolecules upon PEGylation and immunogenicity of PEG triggering immune response and abrogating clinical efficacy, which collectively necessitate development of stealth polymer alternatives. Here we demonstrate that comb-shape poly[oligo(ethylene glycol) methyl ether methacrylate] (POEGMA), a stealth polymer alternative, has a more compact structure than PEG and self-organize into nanoparticles in a molecular weight dependent manner. Most notably, we show that comb-shape POEGMA promotes significantly higher cellular uptake and exhibits less steric hindrance imposed on the conjugated biomolecule than PEG. Collectively, comb-shape POEGMA offers a versatile alternative to PEG for stealth polymer-biomolecule conjugation applications.Article Citation - WoS: 25Citation - Scopus: 23Synthesis and Characterization of Aicar and Dox Conjugated Multifunctional Nanoparticles as a Platform for Synergistic Inhibition of Cancer Cell Growth(American Chemical Society, 2016) Dağlıoğlu, Cenk; Okutucu, BurcuThe success of cancer treatment depends on the response to chemotherapeutic agents. However, malignancies often acquire resistance to drugs if they are used frequently. Combination therapy involving both a chemotherapeutic agent and molecularly targeted therapy may have the ability to retain and enhance therapeutic efficacy. Here, we addressed this issue by examining the efficacy of a novel therapeutic strategy that combines AICAR and DOX within a multifunctional platform. In this context, we reported the bottom-up synthesis of Fe3O4@SiO2(FITC)-FA/AICAR/DOX multifunctional nanoparticles aiming to neutralize survivin (BIRC5) to potentiate the efficacy of DOX against chemoresistance. The structure of nanoparticles was characterized by dynamic light scattering (DLS), zeta-potential measurement, X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FT-IR), thermogravimetric analysis (TGA), and electron microscopy (SEM and STEM with EDX) techniques. Cellular uptake and cytotoxicity experiments demonstrated preferentially targeted delivery of nanoparticles and an efficient reduction of cancer cell viability in five different tumor-derived cell lines (A549, HCT-116, HeLa, Jurkat, and MIA PaCa-2). These results indicate that the multifunctional nanoparticle system possesses high inhibitory drug association and sustained cytotoxic effect with good biocompatibility. This novel approach which combines AICAR and DOX within a single platform might be promising as an antitumor treatment for cancer.Article Citation - WoS: 17Citation - Scopus: 19Cultivar Origin and Admixture Detection in Turkish Olive Oils by Snp-Based Caps Assays(American Chemical Society, 2015) Uncu, Ali Tevfik; Frary, Anne; Doğanlar, SamiThe aim of this study was to establish a DNA-based identification key to ascertain the cultivar origin of Turkish monovarietal olive oils. To reach this aim, we sequenced short fragments from five olive genes for SNP (single nucleotide polymorphism) identification and developed CAPS (cleaved amplified polymorphic DNA) assays for SNPs that alter restriction enzyme recognition motifs. When applied on the oils of 17 olive cultivars, a maximum of five CAPS assays were necessary to discriminate the varietal origin of the samples. We also tested the efficiency and limit of our approach for detecting olive oil admixtures. As a result of the analysis, we were able to detect admixing down to a limit of 20%. The SNP-based CAPS assays developed in this work can be used for testing and verification of the authenticity of Turkish monovarietal olive oils, for olive tree certification, and in germplasm characterization and preservation studies.Article Citation - WoS: 16Citation - Scopus: 17Authentication of Botanical Origin in Herbal Teas by Plastid Noncoding Dna Length Polymorphisms(American Chemical Society, 2015) Uncu, Ali Tevfik; Uncu, Ayşe Özgür; Frary, Anne; Doğanlar, SamiThe aim of this study was to develop a DNA barcode assay to authenticate the botanical origin of herbal teas. To reach this aim, we tested the efficiency of a PCR-capillary electrophoresis (PCR-CE) approach on commercial herbal tea samples using two noncoding plastid barcodes, the trnL intron and the intergenic spacer between trnL and trnF. Barcode DNA length polymorphisms proved successful in authenticating the species origin of herbal teas. We verified the validity of our approach by sequencing species-specific barcode amplicons from herbal tea samples. Moreover, we displayed the utility of PCR-CE assays coupled with sequencing to identify the origin of undeclared plant material in herbal tea samples. The PCR-CE assays proposed in this work can be applied as routine tests for the verification of botanical origin in herbal teas and can be extended to authenticate all types of herbal foodstuffs.Article Citation - WoS: 20Citation - Scopus: 17Differentiation of Normal and Cancer Cell Adhesion on Custom Designed Protein Nanopatterns(American Chemical Society, 2015) Horzum, Utku; Özdil, Berrin; Pesen Okvur, DevrimCell adhesion to the extracellular matrix is deregulated in metastasis. However, traditional surfaces used to study cell adhesion do not faithfully mimic the in vivo microenvironment. Electron beam lithography (EBL) is able to generate customized protein nanopatterns. Here, we used an EBL-based green lithography approach to fabricate homogeneous and gradient, single (fibronectin, K-casein) and double (fibronectin, laminin) active component protein nanopatterns with micrometer scale spacing to investigate differences in adhesion of breast cancer cells (BCC) and normal mammary epithelial cells (NMEC). Our results showed that as expected, in contrast to NMEC, BCC were plastic: they tolerated nonadhesion promoting regions, adapted to flow and exploited gradients better. In addition, the number of focal adhesions but not their area appeared to be the dominant parameter for regulation of cell adhesion. Our findings also demonstrated that custom designed protein nanopatterns, which can properly mimic the in vivo microenvironment, enable realistic distinction of normal and cancerous cell adhesion.Article Citation - WoS: 38Citation - Scopus: 36Structural Studies of Geosmin Synthase, a Bifunctional Sesquiterpene Synthase With ?? Domain Architecture That Catalyzes a Unique Cyclization-Fragmentation Reaction Sequence(American Chemical Society, 2015) Harris, Golda G.; Lombardi, Patrick M.; Pemberton, Travis A.; Matsui, Tsutomu; Weiss, Thomas M.; Cole, Kathryn E.; Köksal, Mustafa; Murphy, Frank V.; Vedula, L. Sangeetha; Chou, Wayne K. W.; Cane, David E.; Christianson, David W.Geosmin synthase from Streptomyces coelicolor (ScGS) catalyzes an unusual, metal-dependent terpenoid cyclization and fragmentation reaction sequence. Two distinct active sites are required for catalysis: the N-terminal domain catalyzes the ionization and cyclization of farnesyl diphosphate to form germacradienol and inorganic pyrophosphate (PPi), and the C-terminal domain catalyzes the protonation, cyclization, and fragmentation of germacradienol to form geosmin and acetone through a retro-Prins reaction. A unique αα domain architecture is predicted for ScGS based on amino acid sequence: each domain contains the metal-binding motifs typical of a class I terpenoid cyclase, and each domain requires Mg2+ for catalysis. Here, we report the X-ray crystal structure of the unliganded N-terminal domain of ScGS and the structure of its complex with three Mg2+ ions and alendronate. These structures highlight conformational changes required for active site closure and catalysis. Although neither full-length ScGS nor constructs of the C-terminal domain could be crystallized, homology models of the C-terminal domain were constructed on the basis of 36% sequence identity with the N-terminal domain. Small-angle X-ray scattering experiments yield low-resolution molecular envelopes into which the N-terminal domain crystal structure and the C-terminal domain homology model were fit, suggesting possible αα domain architectures as frameworks for bifunctional catalysis. © 2015 American Chemical Society.Article Citation - WoS: 66Citation - Scopus: 82Antimicrobial and Antioxidant Activities of Turkish Extra Virgin Olive Oils(American Chemical Society, 2010) Karaosmanoğlu, Hande; Soyer, Ferda; Özen, Banu; Tokatlı, FigenTurkish extra virgin olive oils (EVOO) from different varieties/ geographical origins and their phenolic compounds were investigated in terms of their antimicrobial and antioxidant properties in comparison to refined olive, hazelnut, and canola oils. Antimicrobial activity was tested against three foodborne pathogenic bacteria, Escherichia coli O157:H7, Listeria monocytogenes, and Salmonella Enteritidis. Although all EVOOs showed a bactericidal effect, the individual phenolic compounds demonstrated only slight antimicrobial activity. Moreover, refined oil samples did not show any antimicrobial activity. Among the phenolic compounds, cinnamic acid (2 mg/kg of oil) had the highest percent inhibition value with 0.25 log reduction against L. monocytogenes. The synergistic interactions of tyrosol, vanillin, vanillic, and cinnamic acids were also observed against Salmonella Enteritidis. The antioxidant activities of oils were tested by β-carotene-linoleate model system and ABTS method. In both methods, EVOOs showed higher antioxidant activities, whereas refined oils had lower activity. The ABTS method provided a higher correlation (0.89) with total phenol content. © 2010 American Chemical Society.Article Citation - WoS: 30Citation - Scopus: 32Compartmentalization and Regulation of Mitochondrial Function by Methionine Sulfoxide Reductases in Yeast(American Chemical Society, 2010) Kaya, Alaattin; Koç, Ahmet; Lee, Byung Cheon; Fomenko, Dmitri E.; Rederstorff, Mathieu; Krol, Alain; Lescure, Alain; Gladyshev, Vadim N.Elevated levels of reactive oxygen species can damage proteins. Sulfur-containing amino acid residues, cysteine and methionine, are particularly susceptible to such damage. Various enzymes evolved to protect proteins or repair oxidized residues, including methionine sulfoxide reductases MsrA and MsrB, which reduce methionine (S)-sulfoxide (Met-SO) and methionine (R)-sulfoxide (Met-RO) residues, respectively, back to methionine. Here, we show that MsrA and MsrB are involved in the regulation of mitochondrial function. Saccharomyces cerevisiae mutant cells lacking MsrA, MsrB, or both proteins had normal levels of mitochondria but lower levels of cytochrome c and fewer respiration-competent mitochondria. The growth of single MsrA or MsrB mutants on respiratory carbon sources was inhibited, and that of the double mutant was severely compromised, indicating impairment of mitochondrial function. Although MsrA and MsrB are thought to have similar roles in oxidative protein repair each targeting a diastereomer of methionine sulfoxide, their deletion resulted in different phenotypes. GFP fusions of MsrA and MsrB showed different localization patterns and primarily localized to cytoplasm and mitochondria, respectively. This finding agreed with compartment-specific enrichment of MsrA and MsrB activities. These results show that oxidative stress contributes to mitochondrial dysfunction through oxidation of methionine residues in proteins located in different cellular compartments. © 2010 American Chemical Society.Article Citation - WoS: 17Citation - Scopus: 19Effect of Thioredoxin Deletion and P53 Cysteine Replacement on Human P53 Activity in Wild-Type and Thioredoxin Reductase Null Yeast(American Chemical Society, 2009) Stoner, Christopher S.; Pearson, George D.; Koç, Ahmet; Merwin, Jason R.; Lopez, Nathan I.; Merrill, Gary FredericReporter gene transactivation by human p53 is inhibited in budding yeast lacking the TRR1 gene encoding thioredoxin reductase. To investigate the role of thioredoxin in controlling p53 activity, the level of reporter gene transactivation by p53 was determined in yeast lacking the TRX1 and TRX2 genes encoding cytosolic thioredoxin. Surprisingly, p53 activity was unimpaired in yeast lacking thioredoxin. Subsequent analyses showed that thioredoxin deletion suppressed the inhibitory effect of thioredoxin reductase deletion, suggesting that accumulation of oxidized thioredoxin in mutant yeast was necessary for p53 inhibition. Purified human thioredoxin and p53 interacted in vitro (K d = 0.9 μM thioredoxin). To test the idea that dithio-disulfide exchange reactions between p53 and thioredoxin were responsible for p53 inhibition in mutant yeast, each p53 cysteine was changed to serine, and the effect of the substitution on p53 activity in TRR1 and Δtrr1 yeast was determined. Substitutions at Zn-coordinating cysteines C176, C238, or C242 resulted in p53 inactivation. Unexpectedly, substitution at cysteine C275 also inactivated p53, which was the first evidence for a non-zinc-coordinating cysteine being essential for p53 function. Cysteine substitutions at six positions (C124, C135, C141, C182, C229, and C277) neither inactivated p53 nor relieved the requirement for thioredoxin reductase. Furthermore, no tested combination of these six cysteine substitutions relieved thioredoxin reductase dependence. The results suggested that p53 dependence on thioredoxin reductase either was indirect, perhaps mediated by an upstream activator of p53, or was due to oxidation of one or more of the four essential cysteines.