Viral Kinetics Suggests a Reconciliation of the Disparate Observations of the Modulation of Claudin-1 Expression on Cells Exposed to Hepatitis C Virus

The tight junction protein claudin-1 (CLDN1) is necessary for hepatitis C virus (HCV) entry into target cells. Recent studies have made disparate observations of the modulation of the expression of CLDN1 on cells following infection by HCV. In one study, the mean CLDN1 expression on cells exposed to HCV declined, whereas in another study HCV infected cells showed increased CLDN1 expression compared to uninfected cells. Consequently, the role of HCV in modulating CLDN1 expression, and hence the frequency of cellular superinfection, remains unclear. Here, we present a possible reconciliation of these disparate observations. We hypothesized that viral kinetics and not necessarily HCV-induced receptor modulation underlies these disparate observations. To test this hypothesis, we constructed a mathematical model of viral kinetics in vitro that mimicked the above experiments. Model predictions provided good fits to the observed evolution of the distribution of CLDN1 expression on cells following exposure to HCV. Cells with higher CLDN1 expression were preferentially infected and outgrown by cells with lower CLDN1 expression, resulting in a decline of the mean CLDN1 expression with time. At the same time, because the susceptibility of cells to infection increased with CLDN1 expression, infected cells tended to have higher CLDN1 expression on average than uninfected cells. Our study thus presents an explanation of the disparate observations of CLDN1 expression following HCV infection and points to the importance of considering viral kinetics in future studies of receptor expression on cells exposed to HCV.

Kinetics of adsorption of methylene blue and rhodamine 6G on acrylic acid-based superabsorbents

Superabsorbent polymers (SAPs) of acrylic acid, sodium acrylate, and acrylamide (AM), crosslinked with ethylene glycol dimethacrylate, were synthesized by inverse suspension polymerization. The equilibrium swelling capacities of the SAPs were determined and these decreased with increasing AM content. The adsorption of the two cationic dyes, methylene blue and rhodamine 6G, on the dry as well as equilibrium swollen SAPs was investigated. The amount of the dye adsorbed at equilibrium per unit weight of the SAPs and the rate constants of adsorption were determined. The amount of the dye adsorbed at equilibrium by the SAPs decreased with increasing mol % of AM in the SAPs. The amount of the dye adsorbed at equilibrium was almost equal for the dry and equilibrium swollen SAPs. However, the equilibrium swollen SAPs adsorbed dyes at a higher rate than the dry SAPs. The higher rate of adsorption was attributed to the availability of all the anionic groups present in the fully elongated conformation of the SAPs in the equilibrium swollen state. The effect of initial dye concentration on the adsorption was also investigated and the adsorption was described by Langmuir adsorption isotherms. (C) 2012 Wiley Periodicals, Inc. J Appl Polym Sci, 2012

Thermal degradation kinetics of poly(trimethylol propane triacrylate)/poly(hexane diol diacrylate) interpenetrating polymer network

Interpenetrating polymer networks (IPNs) of trimethylol propane triacrylate (TMPTA) and 1,6-hexane diol diacrylate (HDDA) at different weight ratios were synthesized. Temperature modulated differential scanning calorimetry (TMDSC) was used to determine whether the formation resulted in a copolymer or interpenetrating polymer network (IPN). These polymers are used as binders for microstereolithography (MSL) based ceramic microfabrication. The kinetics of thermal degradation of these polymers are important to optimize the debinding process for fabricating 3D shaped ceramic objects by MSL based rapid prototyping technique. Therefore, thermal and thermo-oxidative degradation of these IPNs have been studied by dynamic and isothermal thermogravimetry (TGA). Non-isothermal model-free kinetic methods have been adopted (isoconversional differential and KAS) to calculate the apparent activation energy (E a) as a function of conversion (α) in N 2 and air. The degradation of these polymers in N 2 atmosphere occurs via two mechanisms. Chain end scission plays a dominant role at lower temperature while the kinetics is governed by random chain scission at higher temperature. Oxidative degradation shows multiple degradation steps having higher activation energy than in N 2. Isothermal degradation was also carried out to predict the reaction model which is found to be decelerating. It was shown that the degradation of PTMPTA follows a contracting sphere reaction model in N 2. However, as the HDDA content increases in the IPNs, the degradation reaction follows Avrami-Erofeev model and diffusion governed mechanisms. The intermediate IPN compositions show both type of mechanism. Based on the above study, debinding strategy for MSL based microfabricated ceramic structure has been proposed. © 2012 Elsevier B.V.

Catalysis of tRNA Aminoacylation: Single Turnover to Steady-State Kinetics of tRNA Synthetases

Aminoacyl-tRNA synthetases (aaRS) catalyze the bimolecular association reaction between amino acid and tRNA by specifically and unerringly choosing the cognate amino acid and tRNA. There are two classes of such synthetases that perform tRNA-aminoacylation reaction. Interestingly, these two classes of aminoacyl-tRNA synthetases differ not only in their structures but they also exhibit remarkably distinct kinetics under pre-steady-state condition. The class I synthetases show initial burst of product formation followed by a slower steady-state rate. This has been argued to represent the influence of slow product release. In contrast, there is no burst in the case of class H enzymes. The tight binding of product with enzyme for class I enzymes is correlated with the enhancement of rate in presence of elongation factor. EF-TU. In spite of extensive experimental studies, there is no detailed theoretical analysis that can provide a quantitative understanding of this important problem. In this article, we present a theoretical investigation of enzyme kinetics for both classes of aminoacyl-tRNA synthetases. We present an augmented kinetic scheme and then employ the methods of time-dependent probability statistics to obtain expressions for the first passage time distribution that gives both the time-dependent and the steady-state rates. The present study quantitatively explains all the above experimental observations. We propose an alternative path way in the case of class II enzymes showing the tRNA-dependent amino acid activation and the discrepancy between the single-turnover and steady-state rate.

Unraveling siRNA unzipping kinetics with graphene

Using all atom molecular dynamics simulations, we report spontaneous unzipping and strong binding of small interfering RNA (siRNA) on graphene. Our dispersion corrected density functional theory based calculations suggest that nucleosides of RNA have stronger attractive interactions with graphene as compared to DNA residues. These stronger interactions force the double stranded siRNA to spontaneously unzip and bind to the graphene surface. Unzipping always nucleates at one end of the siRNA and propagates to the other end after few base-pairs get unzipped. While both the ends get unzipped, the middle part remains in double stranded form because of torsional constraint. Unzipping probability distributions fitted to single exponential function give unzipping time (tau) of the order of few nanoseconds which decrease exponentially with temperature. From the temperature variation of unzipping time we estimate the energy barrier to unzipping. (C) 2012 American Institute of Physics. http://dx.doi.org/10.1063/1.4742189]

High-temperature kinetics of the reaction between CN and hydrocarbons using a novel high-enthalpy flow tube

More than 70 molecules of varied nature have been identified in the envelopes of carbon-rich stars through their spectral fingerprints in the microwave or far infrared regions. Many of them are carbon chain molecules and radicals, and a significant number are unique to the circumstellar medium. The determination of relevant laboratory kinetics data is critical to keep up with the development of the high spectral and spatial resolution observations and of the refinement of chemical models. Neutralneutral reactions of the CN radical with unsaturated hydrocarbons could be a dominant route in the formation of cyanopolyynes, even at low temperatures and deserve a detailed laboratory investigation. The approach we have developed aims to bridge the temperature gap between resistively heated flow tubes and shock tubes. The present kinetic measurements are obtained using a new reactor combining a high-enthalpy source with a flow tube and a pulsed laser photolysislaser-induced fluorescence system to probe the undergoing chemical reactions. The high-enthalpy flow tube has been used to measure the rate constant of the reaction of the CN radical with propane (C3H8), propene (C3H6), allene (C3H4), 1,3-butadiene (1,3-C4H6), and 1-butyne (C4H6) over a temperature range extending from 300 to 1200 K. All studied reactions of CN with unsaturated hydrocarbons are rapid, with rate coefficients greater than 10-10 cm3 center dot molecule-1 center dot s-1 and exhibit slight negative temperature dependence above room temperature. (c) 2012 Wiley Periodicals, Inc. Int J Chem Kinet 44: 753766, 2012

Crystallization and preliminary X-ray studies of MutT1 (MSMEG_2390) from Mycobacterium smegmatis

MutT1 (MSMEG_2390) from Mycobacterium smegmatis has been crystallized and the crystals have been characterized using X-ray diffraction. The crystals belonged to space group P2(1)2(1)2(1). The Matthews coefficient suggested the possibility of one protein molecule in the asymmetric unit of the orthorhombic unit cell. Solution of the structure using the known three-dimensional structure of a bacterial MutT1 is anticipated.

Ex Situ X-ray Diffraction, X-ray Absorption Near Edge Structure, Electron Spin Resonance, and Transmission Electron Microscopy Study of the Hydrothermal Crystallization of Vanadium Oxide Nanotubes: An Insight into the Mechanism of Formation

The nucleation and growth of vanadium oxide nanotubes (VOx-NT) have been followed by a combination of numerous ex situ techniques. long the hydrothermal process. Intermediate solid phases extracted at different reaction times have been characterized by powder X-ray diffraction, scanning and transmission electron microscopy, electron spin resonance, and V-K edge :X-ray absorption near-edge structure spectroscopy. The supernatant vanadate solutions extracted during the hydrothermal treatment have been studied by liquid V-51 NMR and flame. spectroscopy. For short durations of the hydrothermal synthesis, the initial V2O5-surfactant intercalate. is progressively transformed into VOx-NT whose crystallization starts to be detected after a hydrothermal treatment of 24 h. Upon heating from 24 h to 7 days, VOx-NT are obtained in larger amount and with an improved crystallinity. The detection of soluble amines and cyclic metavanadate V4O12](4-) in the supernatant solution along the hydrothermal process suggests that VOx-NT result from a dissolution precipitation mechanism. Metavanadate species V4O12](4-) could behave as molecular precursors in the polymerization reactions leading to VOx-NT.

Thermal degradation kinetics of thermoresponsive poly(N-isopropylacrylamide-co-N,N-dimethylacrylamide) copolymers prepared via RAFT polymerization

Reversible addition-fragmentation chain transfer polymerization at 70 A degrees C in N,N-dimethylformamide was used to prepare poly(N-isopropylacrylamide-co-N,N-dimethylacrylamide) copolymers in various compositions to afford well-defined polymers with pre-determined molecular weight, narrow molecular weight distribution, and precise chain end structure. The copolymer compositions were determined by H-1 NMR spectroscopy. The reactivity ratios of N-isopropylacrylamide (NIPAM) and N,N-dimethylacrylamide (DMA) were calculated as r (NIPAM) = 0.838 and r (DMA) = 1.105, respectively, by the extended Kelen-Tudos method at high conversions. The lower critical solution temperature of PNIPAM can be altered by changing the DMA content in the copolymer chain. Differential scanning calorimetry and thermogravimetric analysis at different heating rates were carried out on these copolymers to understand the nature of thermal degradation and to determine its kinetics. Different kinetic models were applied to estimate various parameters like the activation energy, the order, and the frequency factor. These studies are important to understand the solid state polymer degradation of N-alkyl substituted polymers, which show great potential in the preparation of miscible polymer blends due to their ability to interact through hydrogen bonding.

Cloning, expression, purification, crystallization and preliminary X-ray crystallographic study of thymidylate kinase (TTHA1607) from Thermus thermophilus HB8

Nucleotide biosynthesis plays a key role in cell survival and cell proliferation. Thymidylate kinase is an enzyme that catalyses the conversion of dTMP to dTDP using ATP-Mg2+ as a phosphoryl-donor group. This enzyme is present at the junction of the de novo and salvage pathways; thus, any inhibitor designed against it will result in cell death. This highlights the importance of this enzyme as a drug target. Thymidylate kinase from the extremely thermophilic organism Thermus thermophilus HB8 has been expressed, purified and crystallized using the microbatch method. The crystals diffracted to a resolution of 1.83 angstrom and belonged to the orthorhombic space group P2(1)2(1)2(1), with unit-cell parameters a = 39.50, b = 80.29, c = 122.55 angstrom. Preliminary studies revealed the presence of a dimer in the asymmetric unit with a Matthews coefficient (V-M) of 2.18 angstrom(3) Da(-1).

``On-the-fly'' kinetics of enzymatic racemization using deuterium NMR in DNA-based chiral oriented media

We report the in situ and real-time monitoring of the interconversion of L- and D-alanine-d(3) by alanine racemase from Bacillus stearothermophilus directly observed by H-2 NMR spectroscopy in anisotropic phase. The enantiomers are distinguished by the difference of their H-2 quadrupolar splittings in a chiral liquid crystal containing short DNA fragments. The proof-of-principle, the reliability, and the robustness of this new method is demonstrated by the determination of the turnover rates of the enzyme using the Michaelis Menten model.

Growth kinetics and immune response of chimeric foot-and-mouth disease virus serotype `O' produced through replication competent mini genome of serotype Asia 1, 63/72, in BHK cell lines

Regular vaccinations with potent vaccine, in endemic countries and vaccination to live in non-endemic countries are the methods available to control foot-and-mouth disease. Selection of candidate vaccine strain is not only cumbersome but the candidate should grow well for high potency vaccine preparation. Alternative strategy is to generate an infectious cDNA of a cell culture-adapted virus and use the replicon for development of tailor-made vaccines. We produced a chimeric `O' virus in the backbone of Asia 1 and studied its characteristics. The chimeric virus showed high infectivity titre (>10(10)) in BHK 21 cell lines, revealed small plague morphology and there was no cross reactivity with antiserum against Asia I. The virus multiplies rapidly and reaches peak at 12 h post infection. The vaccine prepared with this virus elicited high antibody titres.

Densification kinetics, phase assemblage and hardness of spark plasma sintered Cu-10 wt% TiB2 and Cu-10 wt% TiB2-10 wt% Pb composites

The present work demonstrates the synthesis of Cu-10 wt% TiB2 composites with a theoretical density of more than 90% by tailoring the spark plasma sintering (SPS) conditions in the temperature range of 400-700 degrees C. Interestingly, 10 wt% Pb addition to Cu-10 wt% TiB2 lowers the sinter density and the difference in the densification behavior of the investigated compositions was discussed in reference to the current profile recorded during a SPS cycle. The sintering kinetics and phase assemblage were also discussed in reference to surface melting of the constituents prior to bulk melting temperature, temperature dependent wettability of Pb on Cu, diffusion kinetics of Cu as well as the formation of various oxides. An important result is that a high hardness of around 2 GPa and relative density close to 92% qtheoretical was achieved for the Cu-10 wt% TiB2-10 wt% Pb composite, and such a combination has never been achieved before using any conventional processing route.

Segmental relaxations and crystallization-induced phase separation in PVDF/PMMA blends in the presence of surface-functionalized multiwall carbon nanotubes

Crystallization-induced phase separation and segmental relaxations in poly(vinylidene fluoride)/poly(methyl methacrylate) (PVDF/PMMA) blends was systematically investigated by melt-rheology and broadband dielectric spectroscopy in the presence of multiwall carbon nanotubes (MWNTs). Different functionalized MWNTs (amine, -NH2; acid, -COOH) were incorporated in the blends by melt-mixing above the melting temperature of PVDF, where the blends are miscible, and the crystallization induced phase separation was probed in situ by shear rheology. Interestingly, only -NH2 functionalized MWNTs (a-MWNTs) aided in the formation of beta-phase (trans-trans) crystals in PVDF, whereas both the neat blends and the blends with -COOH functionalized MWNTs (c-MWNTs) showed only alpha-phase (trans-gauche-trans-gauche') crystals as inferred from wide-angle X-ray diffraction (WXRD) and Fourier transform infrared (FTIR). Furthermore, blends with only a-MWNTs facilitated in heterogeneous nucleation in the blends manifesting in an increase in the calorimetric crystallization temperature and hence, augmented the theologically determined crystallintion induced phase separation temperature. The dielectric relaxations associated with the crystalline phase of PVDF (alpha(c)) was completely absent in the blends with a-MWNTs in contrast to neat blends and the blends with c-MWNTs in the dielectric loss spectra. The relaxations in the blends investigated here appeared to follow Havriliak-Negami (HN) empirical equations, and, more interestingly, the dynamic heterogeneity in the system could be mapped by an extra relaxation at higher frequency at the crystallization-induced phase separation temperature. The mean relaxation time (tau(HN)) was evaluated and observed to be delayed in the presence of MWNTs in the blends, more prominently in the case of blends with a-MWNTs. The latter also showed a significant increase in the dielectric relaxation strength (Delta epsilon). Electron microscopy and selective etching was used to confirm the localization of MWNTs in the amorphous phases of the interspherulitic regions as observed from scanning electron microscopy (SEM). The evolved crystalline morphology, during crystallization-induced phase separation, was observed to have a strong influence on the charge transport processes in the blends. These observations were further supported by the specific interactions (like dipole induced dipole interaction) between a-MWNTs and PVDF, as inferred from FTIR, and the differences in the crystalline morphology as observed from WXRD and polarized optical microscopy (POM).

Temperature dependence of resistance and crystallization in amorphous Si15Te85-xGex thin films

Amorphous thin chalcogenide Si15Te85-xGex films (x: 5, 9, 10, 11, 12) are prepared by flash evaporation and the temperature dependence of resistance of these films has been studied in the temperature range 25-250 degrees C. All the compositions show a linear variation of resistance in this temperature range. Apart from the linear variation, a sharp reduction in resistance at one or at two distinct temperatures (T-TR1/T-TR2) is seen. Thin films annealed at these temperatures, when subjected to X-ray diffraction studies suggest that the dominant crystalline phase at T-TR1 and at T-TR2 is the same and the two dips are associated with varying levels of crystallization. This is also reflected in the atomic force microscopic (AFM) study. Further, the resistance of these two phases shows no drift when the films are annealed for varying lengths of time (10 min to 120 min) suggesting the stability of the phases.