Double-Wronskian solitons and rogue waves for the inhomogeneous nonlinear Schrödinger equation in an inhomogeneous plasma

Plasmas are the main constituent of the Universe and the cause of a vast variety of astrophysical, space and terrestrial phenomena. The inhomogeneous nonlinear Schrödinger equation is hereby investigated, which describes the propagation of an electron plasma wave packet with a large wavelength and small amplitude in a medium with a parabolic density and constant interactional damping. By virtue of the double Wronskian identities, the equation is proved to possess the double-Wronskian soliton solutions. Analytic one- and two-soliton solutions are discussed. Amplitude and velocity of the soliton are related to the damping coefficient. Asymptotic analysis is applied for us to investigate the interaction between the two solitons. Overtaking interaction, head-on interaction and bound state of the two solitons are given. From the non-zero potential Lax pair, the first- and second-order rogue-wave solutions are constructed via a generalized Darboux transformation, and influence of the linear and parabolic density profiles on the background density and amplitude of the rogue wave is discussed.     

Application of atmospheric pressure microwave plasma source for production of hydrogen via methane reforming

In this paper, results of hydrogen production via methane pyrolysis in the atmospheric pressure microwave plasma with CH₄ swirl are presented. A waveguide-based nozzleless cylinder-type microwave plasma source (MPS) was used to convert methane into hydrogen. The plasma generation was stabilized by a CH₄ swirl having a flow rate of 87.5 L min^-1. The absorbed microwave power was 1.5–5 kW. The hydrogen production rate and the corresponding energy efficiency were 866 g (H₂) h^-1 and 577 g (H₂) kWh^-1 of microwave energy absorbed by the plasma, respectively. These parameters are better than our previous results when nitrogen was used as a swirl gas and much better than those typical for other plasma methods of hydrogen production (electron beam, gliding arc, plasmatron).     

Polyphenols and Visual Health: Potential Effects on Degenerative Retinal Diseases

Dietary polyphenols are a group of natural compounds that have been proposed to have beneficial effects on human health. They were first known for their antioxidant properties, but several studies over the years have shown that these compounds can exert protective effects against chronic diseases. Nonetheless, the mechanisms underlying these potential benefits are still uncertain and contradictory effects have been reported. In this review, we analyze the potential effects of polyphenol compounds on some visual diseases, with a special focus on retinal degenerative diseases. Current effective therapies for the treatment of such retinal diseases are lacking and new strategies need to be developed. For this reason, there is currently a renewed interest in finding novel ligands (or known ligands with previously unexpected features) that could bind to retinal photoreceptors and modulate their molecular properties. Some polyphenols, especially flavonoids (e.g., quercetin and tannic acid), could attenuate light-induced receptor damage and promote visual health benefits. Recent evidence suggests that certain flavonoids could help stabilize the correctly folded conformation of the visual photoreceptor protein rhodopsin and offset the deleterious effect of retinitis pigmentosa mutations. In this regard, certain polyphenols, like the flavonoids mentioned before, have been shown to improve the stability, expression, regeneration and folding of rhodopsin mutants in experimental in vitro studies. Moreover, these compounds appear to improve the integration of the receptor into the cell membrane while acting against oxidative stress at the same time. We anticipate that polyphenol compounds can be used to target visual photoreceptor proteins, such as rhodopsin, in a way that has only been recently proposed and that these can be used in novel approaches for the treatment of retinal degenerative diseases like retinitis pigmentosa; however, studies in this field are limited and further research is needed in order to properly characterize the effects of these compounds on retinal degenerative diseases through the proposed mechanisms.     

Characterizing Methyl‐Bearing Side Chain Contacts and Dynamics Mediating Amyloid β Protofibril Interactions Using 13Cmethyl‐DEST and Lifetime Line Broadening

Many details pertaining to the formation and interactions of protein aggregates associated with neurodegenerative diseases are invisible to conventional biophysical techniques. We recently introduced ¹⁵N dark‐state exchange saturation transfer (DEST) and ¹⁵N lifetime line‐broadening to study solution backbone dynamics and position‐specific binding probabilities for amyloid β (Aβ) monomers in exchange with large (2–80 MDa) protofibrillar Aβ aggregates. Here we use ¹³C_methyl DEST and lifetime line‐broadening to probe the interactions and dynamics of methyl‐bearing side chains in the Aβ‐protofibril‐bound state. We show that all methyl groups of Aβ40 populate direct‐contact bound states with a very fast effective transverse relaxation rate, indicative of side‐chain‐mediated direct binding to the protofibril surface. The data are consistent with position‐specific enhancements of ¹³C_methyl‐${R{{{\rm tethered}\hfill \atop 2\hfill}}}$ values in tethered states, providing further insights into the structural ensemble of the protofibril‐bound state.     

Chemical analysis of Gothic mortar from a bridge pier in Roudnice nad Labem (Czech Republic)

In this paper, a Gothic mortar originating from the remains of a bridge pier in Roudnice nad Labem (Czech Republic) was analyzed. The inorganic composition of the mortar showing special mechanical properties was studied using polarizing light microscopy, scanning electron microscopy coupled with energy dispersive X-ray spectrometry, and X-ray diffraction, while the protein content was analyzed by peptide mass mapping using matrix-assisted laser desorption/ionization—time of flight mass spectrometry and nanoliquid chromatography coupled to tandem mass spectrometry. Two types of inorganic binders having a composition similar to mineral wollastonite and hydraulic lime and milk protein additive were detected. We believe that organic and inorganic binders added together to the mortar increase its hardness and firmness in the aquatic environment.     

Protein environmental effects on iron‐sulfur clusters: A set of rules for constructing computational models for inner and outer coordination spheres

The structural properties and reactivity of iron‐sulfur proteins are greatly affected by interactions between the prosthetic groups and the surrounding amino acid residues. Thus, quantum chemical investigations of the structure and properties of protein‐bound iron‐sulfur clusters can be severely limited by truncation of computational models. The aim of this study was to identify, a priori, significant interactions that must be included in a quantum chemical model. Using the [2Fe‐2S] accessory cluster of the FeFe‐hydrogenase as a demonstrative example with rich electronic structural features, the electrostatic and covalent effects of the surrounding side chains, charged groups, and backbone moieties were systematically mapped through density functional theoretical calculations. Electron affinities, spin density differences, and delocalization indexes from the quantum theory of atoms in molecules were used to evaluate the importance of each interaction. Case studies for hydrogen bonding and charged side‐chain interactions were used to develop selection rules regarding the significance of a given protein environmental effect. A set of general rules is proposed for constructing quantum chemical models for iron‐sulfur active sites that capture all significant interactions from the protein environment. This methodology was applied to our previously used models in galactose oxidase and the 6Fe‐cluster of FeFe‐hydrogenase. © 2016 Wiley Periodicals, Inc.     

Isolation of Protein-Nucleic Components of Cotton Chromatin and Investigation of Their Interaction with the Cytokinin-Receptor Complex

Cotton chromatin was fractionated into its components. Fractions of histone proteins, nonhistone proteins (NHp-1, NHp-2, NHp-3), and DNA were obtained. Their interactions with ³ H-BAP and ³ H-BAP-CBP complex were investigated. The RNA-polymerase activities of the obtained fractions were investigated. Fraction NHp-2 was shown to bind specifically hormone and its complex with the receptor. RNA-polymerase was localized in fraction NHp-2     

Thermal Stability of Immobilised α-chymotrypsinogen

The unfolding of α-chymotrypsinogen covalently immobilized on silica beads has been studied by differential scanning calorimetry (DSC). The enzyme undergoes an unfolding transition which, unlike the free protein, cannot be approximated by a single two-state process. After immobilization, the unfolding is characterized by the presence of two partially overlapping transitions, both of them show two-state behavior. The two processes correspond to the separate unfolding of the two domains of the α-chymotrypsinogen molecule. The loss of cooperativity behavior is a consequence of the covalent immobilization. The two domains showed different thermal stability as functions of pH. One of them unfolded with a transition temperature T _m2 higher than T _m of the free enzyme, implying stabilization effect of immobilization. However, below pH 4.5, its native structure is lost. The other transition shows a remarkable pH-independent thermal stability from pH 2.5 to 7.0. This revised version was published online in July 2006 with corrections to the Cover Date.     

Spectroscopic investigation of calcium binding sites in the neurotoxin vipoxin and its components-relation with the X-ray structure

Vipoxin is a neurotoxin from the venom of Vipera ammodytes meridionalis, the most toxic snake in Europe. It is a unique complex of a toxic phospholipase A2 (PLA2) and a non-toxic PLA2-like protein inhibitor (Inh) which probably evolved from the enzyme and reduces its activity and toxicity. The enzymatic activity of Vipoxin is Ca2+-dependent and the interaction of this metal ion with the neurotoxic complex and its separated components was investigated using the fluorescent probe ANS. Vipoxin binds two calcium ions, one per each subunit. The X-ray model of the Ca2+-free neurotoxin shows that the potential metal-binding sites require minor structural changes to bind calcium. The dissociation constants K(2+)Ca of the calcium complexes of Vipoxin and its components, PLA2 and Inh, were determined to be 16, 10 and 9 mM, respectively. The affinity for calcium of Vipoxin is reduced in comparison to those of PLA2 and Inh. The X-ray model shows that the potential Ca2+-binding sites in the two components are partially 'shielded' in the complex. The affinity of the neurotoxin to Sr2+ and Ba2+ is lower and the respective K(2+)Ca are 20 and 30 mM. The saturation of Ca2+-binding sites increased the melting point Tm of Vipoxin by 11 degrees C and the activation energy for the thermal deactivation of the excited tryptophans Ea by 11 kJ mol(-1) x Ca2+ is important not only for the enzymatic activity of Vipoxin but also for its thermostability.     

Down syndrome critical region 1 enhances the proteolytic cleavage of calcineurin

Down syndrome critical region 1 (DSCR1), an oxidative stress-response gene, interacts with calcineurin and represses its phosphatase activity. Recently it was shown that hydrogen peroxide inactivates calcineurin by proteolytic cleavage. Based on these facts, we investigated whether oxidative stress affects DSCR1-mediated inactivation of calcineurin. We determined that overexpression of DSCR1 leads to increased proteolytic cleavage of calcineurin. Convertsely, knockdown of DSCR1 abolished calcineurin cleavage upon treatment with hydrogen peroxide. The PXIIXT motif in the COOH-terminus of DSCR1 is responsible for both binding and cleavage of calcineurin. The knockdown of overexpressed DSCR1 in DS fibroblast cells also abrogated calcineurin proteolysis by hydrogen peroxide. These results suggest that DSCR1 has the ability to inactivate calcineurin by inducing proteolytic cleavage of calcineurin upon oxidative stress.