PubMed İndeksli Yayınlar Koleksiyonu / PubMed Indexed Publications Collection

Permanent URI for this collectionhttps://hdl.handle.net/20.500.14365/2

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Citation - WoS: 3
Citation - Scopus: 3
Atomic Force Microscopy Investigation of the Contributions of Listeria Monocytogenes Cell-Wall Biomacromolecules To Their Adherence and Mechanics
(Amer Chemical Soc, 2020) Gördesli Duatepe, Fatma Pınar; Park, Bong J.; Kawas, Leen H.; Abu-Lail, Nehal, I
In this work, the contributions of the pathogenic Listeria monocytogenes cell-wall biomacromolecules to the bacterial mechanics and adhesion to a model inert surface of silicon nitride in water were investigated by atomic force microscopy. Chemical ethylenediaminetetraacetic acid (EDTA) and biological enzymatic trypsin treatments of cells were performed to partially or totally remove the bacterial cell-wall proteins and carbohydrates. Removal of 48.2% proteins and 29.2% of carbohydrates from the cell-wall of the bacterium by the EDTA treatment resulted in a significant decrease in the length of the bacterial cell-wall biomacromolecules and an increase in the rigidity of the bacterial cells as predicted from fitting a model of steric repulsion to the force-distance approach data and classic Hertz model to the indentation-force data, respectively. In comparison, removal of almost all the cell-wall proteins (99.5% removal) and 8.6% of cell-wall carbohydrates by the trypsin treatment resulted in an increase in the elasticity of the bacterial cells, an increase in the extension of the cell-wall biomacromolecules, and a significant decrease in their apparent grafting densities. In addition, adhesion strength of native-untreated L. monocytogenes to silicon nitride in water decreased by 30% on average after the EDTA treatment and further decreased by 60% on average after the trypsin treatment, showing a positive correlation with the% removal of cell-wall proteins by the EDTA and trypsin treatments, respectively.
Citation - WoS: 16
Dynamics of Spatially Confined Bisphenol a Trimers in a Unimolecular Network on Ag(111)
(Amer Chemical Soc, 2016) Lloyd, Julian A.; Papageorgiou, Anthoula C.; Fischer, Sybille; Oh, Seung Cheol; Saglam, Ozge; Diller, Katharina; Duncan, David A.
Bisphenol A (BPA) aggregates on Ag(111) shows a polymorphism between two supramolecular motifs leading to formation of distinct networks depending on thermal energy. With rising temperature a dimeric pairing scheme reversibly converts into a trimeric motif, which forms a hexagonal superstructure with complex dynamic characteristics. The trimeric arrangements notably organize spontaneously into a self-assembled one-component array with supramolecular BPA rotors embedded in a two-dimensional stator sublattice. By varying the temperature, the speed of the rotors can be controlled as monitored by direct visualization. A combination of scanning tunneling microscopy and dispersion corrected density-functional tight-binding (DFTB-vdW(surf)) based molecular modeling reveals the exact atomistic position of each molecule within the assembly as well as the driving force for the formation of the supramolecular rotors.
Citation - WoS: 10
Citation - Scopus: 12
Responses of Acinetobacter Baumannii Bound and Loose Extracellular Polymeric Substances To Hyperosmotic Agents Combined With or Without Tobramycin: an Atomic Force Microscopy Study
(Amer Chemical Soc, 2019) Deliorman, Muhammedin; Gördesli Duatepe, Fatma Pınar; Davenport, Emily K.; Fransson, Boel A.; Call, Douglas R.; Beyenal, Haluk; Abu-Lail, Nehal I.
In this work, contributions of extracellular polymeric substances (EPS) to the nanoscale mechanisms through which the multidrug-resistant Acinetobacter baumannii responds to antimicrobial and hyperosmotic treatments were investigated by atomic force microscopy. Specifically, the adhesion strengths to a control surface of silicon nitride (Si3N4) and the lengths of bacterial surface biopolymers of bound and loose EPS extracted from A. baumannii biofilms were quantified after individual or synergistic treatments with hyperosmotic agents (NaCl and maltodextrin) and an antibiotic (tobramycin). In the absence of any treatment, the loose EPS were significantly longer in length and higher in adhesion to Si3N4 than the bound EPS. When used individually, the hyperosmotic agents and tobramycin collapsed the A. baumannii bound and loose EPS. The combined treatment of maltodextrin with tobramycin collapsed only the loose EPS and did not alter the adhesion of both bound and loose EPS to Si3N4. In addition, the combined treatment was not as effective in collapsing the EPS molecules as when tobramycin was applied alone. Finally, the effects of treatments were dose-dependent. Altogether, our findings suggest that a sequential treatment could be effective in treating A. baumannii biofilms, in which a hyperosmotic agent is used first to collapse the EPS and limit the diffusion of nutrients into the biofilm, followed by the use of an antibiotic to kill the bacterial cells that escape from the biofilm because of starvation.
Citation - WoS: 57
Citation - Scopus: 74
Single-Image Colorimetric Water Quality Detection Using a Smartphone
(Amer Chemical Soc, 2018) Kilic, Volkan; Alankus, Gazihan; Horzum, Nesrin; Mutlu, Ali Y.; Bayram, Abdullah; Solmaz, Mehmet E.
In this paper, we present a smartphone platform for colorimetric water quality detection based on the use of built-in camera for capturing a single-use reference image. A custom-developed app processes this image for training and creates a reference model to be used later in real experimental conditions to calculate the concentration of the unknown solution. This platform has been tested on four different water quality colorimetric assays with various concentration levels, and results show that the presented platform provides approximately 100% accuracy for colorimetric assays with noticeable color difference. This portable, cost-effective, and user-friendly platform is promising for application in water quality monitoring.
Citation - WoS: 50
Citation - Scopus: 54
Synthesis of Pyrene-Fused Pyrazaacenes on Metal Surfaces: Toward One-Dimensional Conjugated Nanostructures
(Amer Chemical Soc, 2016) Jiang, Li; Papageorgiou, Anthoula C.; Oh, Seung Cheol; Sağlam, Özge; Reichert, Joachim; Duncan, David A.; Zhang, Yi-Qi
We investigated the synthesis of one-dimensional nanostructures via Schiff base (imine) formation on three close-packed coinage metal (Au, Ag, and Cu) surfaces under ultrahigh vacuum conditions. We demonstrate the feasibility of forming pyrene-fused pyrazaacene-based oligomers on the Ag(111) surface by thermal annealing of tetraketone and tetraamine molecules, which were designed to afford cyclocondensation products. Direct visualization by scanning tunneling microscopy of reactants, intermediates, and products with submolecular resolution and the analysis' of their statistical distribution in dependence of stoichiometry and annealing temperature together with the inspection of complementary X-ray photoelectron spectroscopy signatures provide unique insight in the reaction mechanism, its limitations, and the role of the supporting substrate. In contrast to the reaction on Ag(111), the reactants desorb from the Au(111) surface before reacting, whereas they decompose on the Cu(111) Surface during the relevant thermal treatment.

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