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Sangyun Lee, Heather B Mayes, Jessica M J Swanson, Gregory A Voth
The ClC family of transmembrane proteins functions throughout nature to control the transport of Cl- ions across biological membranes. ClC-ec1 from Escherichia coli is an antiporter, coupling the transport of Cl- and H+ ions in opposite directions and driven by the concentration gradients of the ions. Despite keen interest in this protein, the molecular mechanism of the Cl-/H+ coupling has not been fully elucidated. Here, we have used multiscale simulation to help identify the essential mechanism of the Cl-/H+ coupling...
October 26, 2016: Journal of the American Chemical Society
Odete Gonçalves, L Filipe C Castro, Adam J Smolka, António Fontainhas, Jonathan M Wilson
The stomach, which is characterized by acid peptic digestion in vertebrates, has been lost secondarily multiple times in the evolution of the teleost fishes. The Cypriniformes are largely seen as an agastric order; however, within the superfamily Cobitoidea, the closely related sister groups Nemacheilidae and Balitoridae have been identified as gastric families. The presence of these most recently diverged gastric families in an otherwise agastric clade indicates that either multiple (>2-3) loss events occurred with the Cyprinidae, Catostomidae and Cobitidae, or that gastric reinvention arose in a recent ancestor of the Nemacheilidae/Balitoridae sister clade...
2016: PloS One
A Leela Siva Kumari, Alla Siva Reddy, K C Kumara Swamy
An approach to both 1,3- and 1,4-oxazines is developed by the cascade cyclization of epoxy ynamides under transition metal-free conditions. Thus, while 1,3-oxazines are obtained in a regio- and stereoselective manner by using base, cyclization of epoxy ynamides with sodium azide as a nucleophile results in 1,4-oxazines. Deuterium-labeling experiment demonstrates the role of water as a proton source in the formation of 1,4-oxazines. Epoxy tethered alkyne precursors provide 1,4-oxazines that undergo click reaction...
October 26, 2016: Organic Letters
Justyna Czaban-Jóźwiak, Rafał Loska, Mieczyslaw Makosza
Readily available ethyl chlorofluoroacetate, when treated with a strong base, forms an -chloro--fluorocarbanion that adds to nitroarenes at position ortho- or para- to the nitro group with formation of anionic sigmaH-adducts. Subsequent base-induced beta-elimination of HCl proceeds selectively to give nitrobenzylic alpha-fluorocarbanions and then, upon protonation, ethyl alpha-fluoro-alpha-nitroarylacetates.
October 26, 2016: Journal of Organic Chemistry
Vicente Rodríguez-González, Ruth B Domínguez-Espíndola, Sergio Casas-Flores, Olga A Patrón-Soberano, Roberto Camposeco Solis, Soo Wohn Lee
Antifungal silver nanocomposites inspired by titanate nanotubes (AgTNTs) were successfully evaluated for the effective inactivation of the phytopathogenic fungus Botrytis Cinerea within 20 minutes. One dimensional H2Ti3O7 nanotubes functionalized with silver nanoparticles (AgNPs) exhibit unique surface and antifungal properties for the photoinactivation of B. Cinerea. Nanostructured titanates were synthesized by the eco-friendly, practical, microwave-induced, hydrothermal method followed by a highly monodispersive AgNP UV-photodeposition...
October 26, 2016: ACS Applied Materials & Interfaces
Caijuan Wang, Hiroshi Yamamoto, Fumika Narumiya, Yuri Nakajima Munekage, Giovanni Finazzi, Ildiko Szabo, Toshiharu Shikanai
KEA3 is a thylakoid membrane localized K(+) /H(+) antiporter and regulates photosynthesis by modulating two components of proton motive force (pmf), the proton gradient (∆pH) and the electric potential (∆ψ). We identified a mutant allele of KEA3, disturbed proton gradient regulation (dpgr) based on its reduced non-photochemical quenching (NPQ) in artificial (CO2 -free with low O2 ) air. This phenotype was enhanced in the mutant backgrounds of PSI cyclic electron transport (pgr5 and crr2-1). In ambient air, reduced NPQ was observed during induction of photosynthesis in dpgr, the phenotype that was enhanced after overnight dark adaptation...
October 26, 2016: Plant Journal: for Cell and Molecular Biology
Devasena Ponnalagu, Harpreet Singh
Mitochondria are the "power house" of a cell continuously generating ATP to ensure its proper functioning. The constant production of ATP via oxidative phosphorylation demands a large electrochemical force that drives protons across the highly selective and low-permeable mitochondrial inner membrane. Besides the conventional role of generating ATP, mitochondria also play an active role in calcium signaling, generation of reactive oxygen species (ROS), stress responses, and regulation of cell-death pathways...
October 26, 2016: Handbook of Experimental Pharmacology
Christiane Stern, Laurent Castera
Non-invasive diagnosis and quantification of hepatic steatosis rely on two different but complementary approaches: biomarkers or imaging techniques, either ultrasound-based such as liver ultrasonography and controlled attenuation parameter (CAP), or computed tomography (CT) and magnetic resonance imaging (MRI). Scores for the detection of steatosis have not gained much popularity in clinical practice so far. CAP, using the M probe, is the most promising technique but needs to be implemented with the XL probe and compared to ultrasound that, despite its limitations, remains the most widely used method...
October 25, 2016: Hepatology International
Altay Çelebi, Dinçer Aydın, Orhan Kocaman, Buğra Tolga Konduk, Ömer Şentürk, Sadetin Hülagü
BACKGROUND/AIMS: Studies on the therapeutic efficacy of proton pump inhibitors (PPIs) in patients with gastroesophageal reflux disease (GERD) have been recently published. In most of these studies, comparison of only two PPIs have been made. There are few studies on the comparison of four or more PPIs. We aimed to compare the acid inhibitory effects of esomeprazole 40 mg, rabeprazole 20 mg, lansoprazole 30 mg, and pantoprazole 40 mg on days 1 and 5 of treatment in patients with GERD, who were extensive metabolizers in regard to the CYP2C19 genotype...
September 2016: Turkish Journal of Gastroenterology: the Official Journal of Turkish Society of Gastroenterology
Vicki T Taasti, Jørgen B B Petersen, Ludvig P Muren, Jesper Thygesen, David C Hansen
PURPOSE: In this study the authors present a new method for estimation of proton stopping power ratios (SPRs) using dual energy CT (DECT), which is robust toward CT noise. The authors propose a parametrization for SPR based directly on the CT numbers in a DECT image set, whereby the intermediate steps of estimating the relative electron density, ρe, and mean excitation energy, I, are avoided. METHODS: The SPR parametrization proposed in this study is a purely empirical fit based on the theoretical SPR values for a list of 34 reference human tissues...
October 2016: Medical Physics
Jeppe Brage Christensen, Heikki Tölli, Niels Bassler
PURPOSE: Dosimetry with ionization chambers in clinical ion beams for radiation therapy requires correction for recombination effects. However, common radiation protocols discriminate between initial and general recombination and provide no universal correction method for the presence of both recombination types in ion beams of charged particles heavier than protons. The advent of multiple field optimization in ion beams, allowing for complex patterns of dose delivery in both temporal and spatial domains, results in new challenges for recombination correction where the resulting recombination depends on the plan delivered...
October 2016: Medical Physics
Peng Wang, Jochen Cammin, Francesca Bisello, Timothy D Solberg, James E McDonough, Timothy C Zhu, David Menichelli, Boon-Keng Kevin Teo
PURPOSE: Proton radiography (PR) and proton computed tomography (PCT) can be used to measure proton stopping power directly. However, practical and cost effective proton imaging detectors are not widely available. In this study, the authors investigated the feasibility of proton imaging using a silicon diode array. METHODS: A one-dimensional silicon diode detector array (1DSDA) was aligned with the central axis (CAX) of the proton beam. Polymethyl methacrylate (PMMA) slabs were used to find the correspondence between the water equivalent thickness (WET) and 1DSDA channel number...
October 2016: Medical Physics
Christopher Kurz, Florian Kamp, Yang-Kyun Park, Christoph Zöllner, Simon Rit, David Hansen, Mark Podesta, Gregory C Sharp, Minglun Li, Michael Reiner, Jan Hofmaier, Sebastian Neppl, Christian Thieke, Reinoud Nijhuis, Ute Ganswindt, Claus Belka, Brian A Winey, Katia Parodi, Guillaume Landry
PURPOSE: This work aims at investigating intensity corrected cone-beam x-ray computed tomography (CBCT) images for accurate dose calculation in adaptive intensity modulated proton therapy (IMPT) for prostate and head and neck (H&N) cancer. A deformable image registration (DIR)-based method and a scatter correction approach using the image data obtained from DIR as prior are characterized and compared on the basis of the same clinical patient cohort for the first time. METHODS: Planning CT (pCT) and daily CBCT data (reconstructed images and measured projections) of four H&N and four prostate cancer patients have been considered in this study...
October 2016: Medical Physics
Steven Michiels, Antoine D'Hollander, Nicolas Lammens, Mathias Kersemans, Guozhi Zhang, Jean-Marc Denis, Kenneth Poels, Edmond Sterpin, Sandra Nuyts, Karin Haustermans, Tom Depuydt
PURPOSE: 3D printing technology is investigated for the purpose of patient immobilization during proton therapy. It potentially enables a merge of patient immobilization, bolus range shifting, and other functions into one single patient-specific structure. In this first step, a set of 3D printed materials is characterized in detail, in terms of structural and radiological properties, elemental composition, directional dependence, and structural changes induced by radiation damage. These data will serve as inputs for the design of 3D printed immobilization structure prototypes...
October 2016: Medical Physics
Marta Tarkanovskaja, Kuno Kooser, Helena Levola, Ergo Nõmmiste, Edwin Kukk
Photofragmentation of small gas-phase acetamide clusters (CH3CONH2)n (n ≤ 10) produced by a supersonic expansion source has been studied using time-of-flight ion mass spectroscopy combined with tunable vacuum-ultraviolet (VUV) synchrotron radiation. Fragmentation channels of acetamide clusters under VUV photoionization resulting in protonated and ammoniated clusters formation were identified with the discussion about the preceding intramolecular rearrangements. Acetamide-2,2,2-d3 clusters were also studied in an experiment with a gas discharge lamp as a VUV light source; comparison with the main experiment gave insights into the mechanism of formation of protonated acetamide clusters, indicating that proton transfer from amino group plays a dominant role in that process...
September 28, 2016: Journal of Chemical Physics
Irina V Fedorova, Michael A Krestyaninov, Lyubov P Safonova
Car-Parrinello molecular dynamics simulations of phosphoric acid (H3PO4)-N,N-dimethylformamide (DMF) mixtures over the whole composition range have been carried out. It has been found that the neutral molecules are the dominant species in this system. The concentration dependences of the average number of H-bonds per proton acceptor atom in P=O and C=O groups as well as per proton donor atom in DMFH(+) ions towards phosphate species have been discussed. The H-bonding between components in all investigated mixtures of H3PO4 and DMF is possible...
September 28, 2016: Journal of Chemical Physics
Ryuichi Okamoto, Akira Onuki
We investigate ionization at a solid-water interface in an applied electric field. We attach an electrode to a dielectric film bearing silanol or carboxyl groups with an areal density Γ0, where the degree of dissociation α is determined by the proton density in water close to the film. We show how α depends on the density n0 of NaOH in water and the surface charge density σm on the electrode. For σm > 0, the protons are expelled away from the film, leading to an increase in α. In particular, in the range 0 < σm < eΓ0, self-regulation occurs to realize α ≅ σm/eΓ0 for n0 ≪ nc, where nc is 0...
September 28, 2016: Journal of Chemical Physics
Rajib Biswas, William Carpenter, Gregory A Voth, Andrei Tokmakoff
Infrared (IR) spectroscopy of the water O-H stretch has been widely used to probe both the local hydrogen-bonding structure and dynamics of aqueous systems. Although of significant interest, the IR spectroscopy of excess protons in water remains difficult to assign as a result of extensive and strong intermolecular interactions in hydrated proton complexes. As an alternate approach, we develop a mixed quantum-classical model for the vibrational spectroscopy of the excess proton in isotopically dilute water that draws on frozen proton-water clusters taken from reactive molecular dynamics trajectories of the latest generation multi-state empirical valence bond proton model (MS-EVB 3...
October 21, 2016: Journal of Chemical Physics
Olga Gorlova, Joseph W DePalma, Conrad T Wolke, Antonio Brathwaite, Tuguldur T Odbadrakh, Kenneth D Jordan, Anne B McCoy, Mark A Johnson
We report the isotope-dependent vibrational predissociation spectra of the H2-tagged OH(-) ⋅ (H2O)n=2,3 clusters, from which we determine the strongly coordination-dependent energies of the fundamentals due to the OH groups bound to the ion and the intramolecular bending modes of the water molecules. The HOH bending fundamental is completely missing in the delocalized OH(-) ⋅ (H2O) binary complex but is recovered upon adding the second water molecule, thereby establishing that the dihydrate behaves as a hydroxide ion solvated by two essentially intact water molecules...
October 7, 2016: Journal of Chemical Physics
István Szabó, Gábor Czakó
We report a detailed quasiclassical trajectory study for the dynamics of the ground-state and CH/CD stretching-excited F(-) + CHD2Cl(vCH/CD = 0, 1) → Cl(-) + CHD2F, HF + CD2Cl(-), and DF + CHDCl(-) SN2, proton-, and deuteron-abstraction reactions using a full-dimensional global ab initio analytical potential energy surface. The simulations show that (a) CHD2Cl(vCH/CD = 1), especially for vCH = 1, maintains its mode-specific excited character prior to interaction, (b) the SN2 reaction is vibrationally mode-specific,...
October 7, 2016: Journal of Chemical Physics
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