Kinetics of the oxidation of thymine and thymidine by triplet 2,2'-dipyridyl in aqueous solutions at different pH values.
Ontology highlight
ABSTRACT:
SUBMITTER: Nguyen TX
PROVIDER: S-EPMC3751068 | biostudies-other | 2013 Aug
REPOSITORIES: biostudies-other
Similar Datasets
Project description:Given that transition metals are essential cofactors in central biological processes, misallocation of the wrong metal ion to a metalloprotein can have resounding and often detrimental effects on diverse aspects of cellular physiology. Therefore, in an attempt to characterize unique and shared responses to chemically similar metals we have reconstructed physiological behaviors of Halobacterium NRC-1, an archaeal halophile, in sub-lethal levels of Mn(II), Fe(II), Co(II), Ni(II), Cu(II) and Zn(II). Over 20% of all genes responded transiently within minutes of exposure to Fe(II), perhaps reflecting immediate large scale physiological adjustments to maintain homeostasis. At steady state, each transition metal induced growth arrest, attempts to minimize oxidative stress, toxic ion scavenging, increased protein turnover and DNA repair, and modulation of active ion transport. While several of these constitute generalized stress responses, up regulation of active efflux of Co(II), Ni(II), Cu(II), and Zn(II), down regulation of Mn(II) uptake and up regulation of Fe(II) chelation, confer resistance to the respective metals. We have synthesized all these discoveries into a unified systems level model to provide an integrated perspective of responses to six transition metals with emphasis on experimentally verified regulatory mechanisms. Finally, through comparisons across global transcriptional responses to different metals we provide insights into putative in vivo metal selectivity of metalloregulatory proteins and demonstrate that a systems approach can help rapidly unravel novel metabolic potential and regulatory programs of poorly studied organisms. Keywords: stress response, dose response
2006-05-31 | GSE4897 | GEO
Project description:The quality of stored frozen products such as foods and biomaterials generally degrades in time due to the growth of large ice crystals by recrystallization. While there is ample experimental evidence that recrystallization within such products (or model systems thereof) is often dominated by diffusion-limited Ostwald ripening, the application of Ostwald-ripening theories to predict measured recrystallization rates has only met with limited success. For a model system of polycrystalline ice within an aqueous solution of sugars, we here show recrystallization rates can be predicted on the basis of Ostwald ripening theory, provided (1) the theory accounts for the fact the solution can be nonideal, nondilute and of different density than the crystals, (2) the effect of ice-phase volume fraction on the diffusional flux of water between crystals is accurately described, and (3) all relevant material properties (involving binary Fick diffusion coefficients, the thermodynamic factor of the solution, and the surface energy of ice) are carefully estimated. To enable calculation of material properties, we derive an alternative formulation of Ostwald ripening in terms of the Maxwell-Stefan instead of the Fick approach to diffusion. First, this leads to a cancellation of the thermodynamic factor (a measure for the nonideality of a solution), which is a notoriously difficult property to obtain. Second, we show that Maxwell-Stefan diffusion coefficients can to a reasonable approximation be related to self-diffusion coefficients, which are relatively easy to measure or predict in comparison to Fick diffusion coefficients. Our approach is validated for a binary system of water and sucrose, for which we show predicted recrystallization rates of ice compare well to experimental results, with relative deviations of at most a factor of 2.
| S-EPMC5890316 | biostudies-literature
Project description:Controlling the pH at the microliter scale can be useful for applications in research, medicine, and industry, and therefore represents a valuable application for synthetic biology and microfluidics. The presented vesicular system translates light of different colors into specific pH changes in the surrounding solution. It works with the two light-driven proton pumps bacteriorhodopsin and blue light-absorbing proteorhodopsin Med12, that are oriented in opposite directions in the lipid membrane. A computer-controlled measuring device implements a feedback loop for automatic adjustment and maintenance of a selected pH value. A pH range spanning more than two units can be established, providing fine temporal and pH resolution. As an application example, a pH-sensitive enzyme reaction is presented where the light color controls the reaction progress. In summary, light color-controlled pH-adjustment using engineered proteoliposomes opens new possibilities to control processes at the microliter scale in different contexts, such as in synthetic biology applications.
| S-EPMC11022694 | biostudies-literature
Project description:1. Osmium tetroxide in dilute ammonia oxidizes various pyrimidine nucleosides at different rates. Thymidine is oxidized about 45 times as fast as deoxycytidine. The phosphate groups may be eliminated from oxidized thymine nucleotides by successive treatments with alkali and then with diphenylamine in aqueous formic acid. The reactions can be applied to the selective degradation of thymidine in oligodeoxynucleotides.
| S-EPMC1264796 | biostudies-other
Project description:Hexazinone, a globally applied broad-spectrum triazine herbicide, has not been mechanistically investigated previously under advanced oxidation processes (AOPs) and adsorption on activated carbon. In this study, its fate during UV-based oxidation with/without hydrogen peroxide (H2O2) and adsorption on coconut shell-based granular activated carbon (CSGAC) in water matrices was investigated. A comparison between various irradiation sources (visible, UVA, UVB, and UVC) revealed the highest degradation rate under UVC. More than 98% degradation of hexazinone was observed under 3 J cm-2 UVC fluence in the presence of 0.5 mM H2O2 at pH 7. Moreover, the degradation rate enhanced significantly with an increase in the initial dosage of H2O2, UV fluence, and contact time in the UV/H2O2 process. The rate of degradation was lower using secondary effluent than that of Milli-Q water due to the presence of dissolved organics in wastewater. However, the reactions in both matrices obeyed pseudo-first-order kinetics. The effect of different scavengers, including methanol, potassium iodide (KI), and tert-butyl alcohol (TBA), showed that hydroxyl radicals (•OH) played a dominant role in hexazinone degradation in the UV/H2O2 process. Hexazinone was effectively adsorbed by CSGAC through π-π electron donor-acceptor interactions between hexazinone's triazine ring and CSGAC's surface functional groups. The isotherm and kinetic studies showed that the adsorption followed the Freundlich model and pseudo-second-order reaction, respectively, suggesting chemisorption. This study provided mechanistic insights on the removal of hexazinone at the tertiary stage of wastewater treatment or the advanced treatment of wastewater reuse.
| S-EPMC9252970 | biostudies-literature
Project description:Reactions involving hydrophobic reactants in water can be much accelerated in organic solvent-free solutions containing amphiphiles at neutral pH and room temperature. Previously, we demonstrated that organosilica colloidal particles could be conveniently synthesized by a versatile salt-catalysis method in solutions modified with various amphiphilic molecules. The method precludes the use of any solvent, any added form of energy (thermal or mechanical), and any strong (or hazardous) acids/bases. Herein, the kinetic properties of the reaction were systematically investigated for fluoride-catalysed synthesis of colloidal organosilica from a thiol-functionalized organosilane precursor, (3-mercaptopropyl)trimethoxysilane. Continuous, real-time ATR-FTIR measurements allowed probing the time evolution of organosilica condensation in different reaction systems, containing one of the following: non-ionic surfactants (Tween 20, Tween 40, Tween 60, Tween 80, Triton X-100), anionic surfactant (sodium dodecyl sulphate; SDS), cationic surfactant (cetyltrimethylammonium bromide; CTAB), and amphiphilic polymers (polyvinyl alcohol and polyvinylpyrrolidone). Overall, while some amphiphile-specific properties were revealed, fluoride-catalysed synthesis was ultrafast with a universal two-phase kinetic scheme (e.g. transition within 5-10 min) for all amphiphiles studied.
| S-EPMC9070784 | biostudies-literature
Project description:Hydrogen generation rate is one of the most important parameters which must be considered for the development of engineering solutions in the field of hydrogen energy applications. In this paper, the kinetics of hydrogen generation from oxidation of hydrogenated porous silicon nanopowders in water are analyzed in detail. The splitting of the Si-H bonds of the nanopowders and water molecules during the oxidation reaction results in powerful hydrogen generation. The described technology is shown to be perfectly tunable and allows us to manage the kinetics by: (i) varying size distribution and porosity of silicon nanoparticles; (ii) chemical composition of oxidizing solutions; (iii) ambient temperature. In particular, hydrogen release below 0 °C is one of the significant advantages of such a technological way of performing hydrogen generation.
| S-EPMC7408030 | biostudies-literature
Project description:Amphoteric statistical equivalent copolymers (P(2VP/NaSS) n ) composed of 2-vinylpyridine (2VP) and anionic sodium p-styrenesulfonate (NaSS) were prepared via reversible addition-fragmentation chain transfer polymerization. The degrees of polymerization (n) were 19 and 95. The monomer reactivity ratio, time conversion profile, and 1H nuclear magnetic resonance diffusion-ordered spectra suggested that the copolymerization of 2VP and NaSS provided statistical or near to random copolymers. P(2VP/NaSS) n exhibited an upper critical solution temperature (UCST) in acidic aqueous solutions on the basis of the charge interactions between the protonated cationic 2VP and anionic NaSS units. With an increase in pH value, the interaction was weakened because of the deprotonation of the 2VP units, thus reducing the UCST. At high [NaCl], the electrostatic interactions among the polymers were weakened because of the screening effect, and again, the UCST was reduced. With an increase in polymer concentration, the intra- and interpolymer interactions increased because of some entanglement, and the UCST consequently increased. Electrostatic interactions among the polymer chains with high molecular weight occurred easier than those among the low-molecular-weight polymer chains, which increased the UCST. The UCST also increased when deuterium oxide was used instead of hydrogen oxide, which was due to the isotopic effect. Hence, the UCST of P(2VP/NaSS) n can be adjusted according to the desired application.
| S-EPMC8028163 | biostudies-literature
Project description:There are many examples of bioactive, disulfide-rich peptides and proteins whose biological activity relies on proper disulfide connectivity. Regioselective disulfide bond formation is a strategy for the synthesis of these bioactive peptides, but many of these methods suffer from a lack of orthogonality between pairs of protected cysteine (Cys) residues, efficiency, and high yields. Here, we show the utilization of 2,2'-dipyridyl diselenide (PySeSePy) as a chemical tool for the removal of Cys-protecting groups and regioselective formation of disulfide bonds in peptides. We found that peptides containing either Cys(Mob) or Cys(Acm) groups treated with PySeSePy in trifluoroacetic acid (TFA) (with or without triisopropylsilane (TIS) were converted to Cys-S-SePy adducts at 37 °C and various incubation times. This novel Cys-S-SePy adduct is able to be chemoselectively reduced by five-fold excess ascorbate at pH 4.5, a condition that should spare already installed peptide disulfide bonds from reduction. This chemoselective reduction by ascorbate will undoubtedly find utility in numerous biotechnological applications. We applied our new chemistry to the iodine-free synthesis of the human intestinal hormone guanylin, which contains two disulfide bonds. While we originally envisioned using ascorbate to chemoselectively reduce one of the formed Cys-S-SePy adducts to catalyze disulfide bond formation, we found that when pairs of Cys(Acm) residues were treated with PySeSePy in TFA, the second disulfide bond formed spontaneously. Spontaneous formation of the second disulfide is most likely driven by the formation of the thermodynamically favored diselenide (PySeSePy) from the two Cys-S-SePy adducts. Thus, we have developed a one-pot method for concomitant deprotection and disulfide bond formation of Cys(Acm) pairs in the presence of an existing disulfide bond.
| S-EPMC7509986 | biostudies-literature
Project description:Diffusion controlled chemical reactions are usually observed in three dimensional media. In contrast, planar bimolecular reactions taking place between reagents adsorbed at a soft interface are two-dimensional and therefore cannot be studied within the same formalism. Indeed, soft interfaces allow the adsorbed species to freely diffuse in a liquid-like manner. Here, we present the first experimental observation of a diffusion-controlled reaction in an environment that is planar at the ångström scale. By means of time-resolved surface second harmonic generation, an inherently surface sensitive technique, we observed that the kinetics of the diffusion of the reagents in the plane decreases as the surface concentration of adsorbed species increases. This is of course not the case for bulk reactions where the rates always increase with the reactant concentration. Such changes in the kinetics regime were rationalised as the evolution from a regular 2D free diffusion regime to a geometry-controlled scheme.
| S-EPMC6761882 | biostudies-other