Subunit interactions in coordination of Ni2+ in cyclic nucleotide-gated channels.

Cyclic nucleotide-gated (CNG) channels present a unique model for studying the molecular mechanisms of channel gating. We have studied the mechanism of potentiation of expressed rod CNG channels by Ni2+ as a first step toward understanding the channel gating process. Here we report that coordination of Ni2+ between histidine residues (H420) on adjacent channel subunits occurs when the channels are open. Mutation of H420 to lysine completely eliminated the potentiation by Ni2+ but did not markedly alter the apparent cGMP affinity of the channel, indicating that the introduction of positive charge at the Ni(2+)-binding site was not sufficient to produce potentiation. Deletion or mutation of most of the other histidines present in the channel did not diminish potentiation by Ni2+. We studied the role of subunit interactions in Ni2+ potentiation by generating heteromultimeric channels using tandem dimers of the rod CNG channel sequence. Injection of single heterodimers in which one subunit contained H420 and the other did not (wt/H420Q or H420Q/wt) resulted in channels that were not potentiated by Ni2+. However, coinjection of both heterodimers into Xenopus oocytes resulted in channels that exhibited potentiation. The H420 residues probably occurred predominantly in nonadjacent subunits when each heterodimer was injected individually, but, when the two heterodimers were coinjected, the H420 residues could occur in adjacent subunits as well. These results suggest that the mechanism of Ni2+ potentiation involves intersubunit coordination of Ni2+ by H420. Based on the preferential binding of Ni2+ to open channels, we suggest that alignment of H420 residues of neighboring subunits into the Ni(2+)-coordinating position may be associated with channel opening.

A secondary-structure model for the self-cleaving region of Neurospora VS RNA.

Neurospora VS RNA performs an RNA-mediated self-cleavage reaction whose products contain 2',3'-cyclic phosphate and 5'-hydroxyl termini. This reaction is similar to those of hammerhead, hairpin, and hepatitis delta virus ribozymes; however, VS RNA is not similar in sequence to these other self-cleaving motifs. Here we propose a model for the secondary structure of the self-cleaving region of VS RNA, supported by site-directed mutagenesis and chemical modification structure probing data. The secondary structure of VS RNA is distinct from those of the other naturally occurring RNA self-cleaving domains. In addition to a unique secondary structure, several Mg-dependent interactions occur during the folding of VS RNA into its active tertiary conformation.

Numerical and experimental investigation of structural stiffness influence on ratcheting convection cell in granular soils under cyclic loading

Lateral cyclic loaded structures in granular soils can lead to an accumulation of irreversible strains by changing their mechanical response (densification) and forming a closed convective cell in the upper layer of the bedding. In the present thesis the convective cell dimension, formation and grain migration inside this closed volume have been studied and presented in relation to structural stiffness and different loads. This relation was experimentally investigated by applying a cyclic lateral force to a scaled flexible vertical element embedded in dry granular soil. The model was monitored with a camera in order to derive the displacement field by means of the PIV technique. Modelling large soil deformation turns out to be difficult, using mesh-based methods. Consequently, a mesh-free approach (DEM) was chosen in order to investigate the granular flow with the aim of extracting interesting micromechanical information. In both the numerical and experimental analyses the effect of different loading magnitudes and different dimensions of the vertical element were considered. The main results regarded the different development, shape and dimensions of the convection cell and the surface settlements. Moreover, the Discrete Element Method has proven to give satisfactory results in the modelling of large deformation phenomena such as the ratcheting convective cell.

Mode Localization in a Nearly Cyclic Symmetric System

Thesis (Ph.D.)--University of Washington, 2016-06

The cyclic antimicrobial peptide RTD-1 induces stabilized lipid-peptide domains more efficiently than its open-chain analogue

The effects of a mammalian cyclic antimicrobial peptide, rhesus theta defensin 1 (RTD-1) and its open chain analogue (oRTD-1), on the phase behaviour and structure of model membrane systems (dipalmitoyl phosphatidylcholine, DPPC and dipalmitoyl phosphatidylglycerol, DPPG) were studied. The increased selectivity of RTD-1 for anionic DPPG over zwitterionic DPPC was shown by differential scanning calorimetry. RTD-1, at a molar peptide-lipid ratio of 1:100, induced considerable changes in the phase behaviour of DPPG, but not of DPPC. The main transition temperature, T-m, Was unchanged, but additional phase transitions appeared above T-m. oRTD-1 induced similar effects. However, the effects were not observable below a peptide:lipid molar ratio of 1:50, which correlates with the weaker biological activity of oRTD-1. Small-and wide-angle X-ray scattering revealed for DPPG the appearance of additional structural features induced by RTP-1 above T-m, which were interpreted as correlated lamellar structures, with increased order of the fatty acyl side chains of the lipid. It is proposed that after initial electrostatic interaction of the cationic rim of the peptide with the anionic DPPG headgroups, leading to stabilized lipid-peptide clusters, the hydrophobic face of the peptide assists in its interaction with the fatty acyl side chains eventually leading to membrane disruption. (C) 2004 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

Studies on the membrane interactions of the cyclotides kalata B1 and kalata B6 on model membrane systems by surface plasmon resonance

In this study we have demonstrated the interactions of kalata B1 and its naturally occurring analogue kalata B6 with five model lipid membranes and have analyzed the binding kinetics using surface plasmon resonance. Two kalata peptides showed a higher affinity for the phosphatidylethanolamine-containing membranes, indicating that the peptides would bind selectively to bacterial membranes. Also we have optimized the procedure for the immobilization of five liposome mixtures and have shown that the procedure provides reproducible levels of immobilized liposomes and could be used to screen the selective binding of putative antimicrobial peptides to model mammalian or microbial phospholipid membranes. (C) 2004 Elsevier Inc. All rights reserved.

Artificial pumping errors in the Kool-Parker scaling model of soil moisture hysteresis

Hysteresis models that eliminate the artificial pumping errors associated with the Kool-Parker (KP) soil moisture hysteresis model, such as the Parker-Lenhard (PL) method, can be computationally demanding in unsaturated transport models since they need to retain the wetting-drying history of the system. The pumping errors in these models need to be eliminated for correct simulation of cyclical systems (e.g. transport above a tidally forced watertable, infiltration and redistribution under periodic irrigation) if the soils exhibit significant hysteresis. A modification is made here to the PL method that allows it to be more readily applied to numerical models by eliminating the need to store a large number of soil moisture reversal points. The modified-PL method largely eliminates any artificial pumping error and so essentially retains the accuracy of the original PL approach. The modified-PL method is implemented in HYDRUS-1D (version 2.0), which is then used to simulate cyclic capillary fringe dynamics to show the influence of removing artificial pumping errors and to demonstrate the ease of implementation. Artificial pumping errors are shown to be significant for the soils and system characteristics used here in numerical experiments of transport above a fluctuating watertable. (c) 2005 Elsevier B.V. All rights reserved.

Studies of the cationic polymerisation of vinylic and energetic cyclic ether monomers

The cationic polymerisation of various monomers, including cyclic ethers bearing energetic nitrate ester (-ON02) groups, substituted styrenes and isobutylene has been investigated. The main reaction studied has been the ring-opening polymerisation of 3- (nitratomethyl)-3-methyl oxetane (NIMMO) using the alcohol/BF3.0Et2 binary initiator system. A series of di-, tri- and tetrafunctional telechelic polymers has been synthesised. In order to optimise the system, achieve controlled molecular weight polymers and understand the mechanism of polymerisation the effects of certain parameters on the molecular weight distribution, as determined by Size Exclusion Chromatography, have been examined. This shows the molecular weight achieved depends on a combination of factors including -OH concentration, addition rate of monomer and, most importantly, temperature. A lower temperature and OH concentration tends to produce higher molecular weight, whereas, slower addition rates of monomer, either have no significant effect or produce a lower molecular weight polymer. These factors were used to increase the formation of a cyclic oligomer, by a side reaction, and suggest, that the polymerisation of NIMMO is complicated with endbiting and back biting reactions, along with other transfer/termination processes. These observations appear to fit the model of an active-chain end mechanism. Another cyclic monomer, glycidyl nitrate (GLYN), has been polymerised by the activated monomer mechanism. Various other monomers have been used to end-cap the polymer chains to produce hydroxy ends which are expected to form more stable urethane links, than the glycidyl nitrate ends, when cured with isocyanates. A novel monomer, butadiene oxide dinitrate (BODN), has been prepared and its homopolymerisation and copolymerisation with GL YN studied. In concurrent work the carbocationic polymerisations of isobutylene or substituted styrenes have been studied. Materials with narrow molecular weight distributions have been prepared using the diphenyl phosphate/BCl3 initiator. These systems and monomers are expected to be used in the synthesis of thermoplastic elastomers.

Hydrogels containing linear and cyclic polyethers

Hydrogels are a unique class of polymer which swell, but do not dissolve in, water. A range of 2-hydroxyethyl methacrylate based copolymer hydrogels containing both cyclic and linear polyethers have been synthesised and are described in this thesis. Initially, cyclic polyethers were occluded within the polymer matrix and the transport properties investigated. The results indicated that the presence of an ionophore can be used to modulate ion transport and that ion transport is described by a dual-sorption mechanism. However, these studies were limited due to ionophore loss during hydration. Hence, the synthesis of a range of acrylate based crown ether monomers was considered. A pure sample of 4-acryolylaminobenzo-15-crown-5 was obtained and a terpolymer containing this monomer was prepared. Transport studies illustrated that the presence of a `bound' ionophore modulates ion transport in a similar way to the occluded systems. The transport properties of a series of terpolymers containing linear polyethers were then investigated. The results indicated that the dual-sorption mechanism is observed for these systems with group II metal cations while the transport of group I metal cations, with the exception of sodium, is enhanced. Finally, the equilibrium water contents (EWC) surface and mechanical properties of these terpolymers containing linear polyethers were examined. Although subtle variations in EWC are observed as the structure of the polyether side chain varies, generally EWC is enhanced due to the hydrophilicity of the polyether side chain. The macroscopic surface properties were investigated using a sessile drop technique and FTIR spectroscopy. At a molecular level surface properties were probed using an in vitro ocular spoilation model and preliminary cell adhesion studies. The results indicate that the polyethylene oxide side chains are expressed at the polymer surface thus reducing the adhesion of biological species.

Exploration by Means of Computer Simulation of Nonlinear Hierarchical Structure of Neuronal Memory on the Model of Olfactory Bulb

Results of numerical experiments are introduced. Experiments were carried out by means of computer simulation on olfactory bulb for the purpose of checking of thinking mechanisms conceptual model, introduced in [2]. Key role of quasisymbol neurons in processes of pattern identification, existence of mental view, functions of cyclic connections between symbol and quasisymbol neurons as short-term memory, important role of synaptic plasticity in learning processes are confirmed numerically. Correctness of fundamental ideas put in base of conceptual model is confirmed on olfactory bulb at quantitative level.

Competitive processes in controlled cationic ring-opening polymerization of oxetane:a Lotka-Volterra predator-prey model of two growing species competing for the same resources

The activation-deactivation pseudo-equilibrium coefficient Qt and constant K0 (=Qt x PaT1,t = ([A1]x[Ox])/([T1]x[T])) as well as the factor of activation (PaT1,t) and rate constants of elementary steps reactions that govern the increase of Mn with conversion in controlled cationic ring-opening polymerization of oxetane (Ox) in 1,4-dioxane (1,4-D) and in tetrahydropyran (THP) (i.e. cyclic ethers which have no homopolymerizability (T)) were determined using terminal-model kinetics. We show analytically that the dynamic behavior of the two growing species (A1 and T1) competing for the same resources (Ox and T) follows a Lotka-Volterra model of predator-prey interactions. © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Work Extraction and Energy Storage in the Dicke Model

We study work extraction from the Dicke model achieved using simple unitary cyclic transformations keeping into account both a non optimal unitary protocol, and the energetic cost of creating the initial state. By analyzing the role of entanglement, we find that highly entangled states can be inefficient for energy storage when considering the energetic cost of creating the state. Such surprising result holds notwithstanding the fact that the criticality of the model at hand can sensibly improve the extraction of work. While showing the advantages of using a many-body system for work extraction, our results demonstrate that entanglement is not necessarily advantageous for energy storage purposes, when non optimal processes are considered. Our work shows the importance of better understanding the complex interconnections between non-equilibrium thermodynamics of quantum systems and correlations among their subparts.

A simplified finite element model for assessing steel fibre reinforced concrete structural performance

The present numerical investigation offers evidence concerning the validity and objectivity of the predictions of a simple, yet practical, finite element model concerning the responses of steel fibre reinforced concrete structural elements under static monotonic and cyclic loading. Emphasis is focused on realistically describing the fully brittle tensile behaviour of plain concrete and the contribution of steel fibres on the post-cracking behaviour it exhibits. The good correlation exhibited between the numerical predictions and their experimental counterparts reveals that, despite its simplicity, the subject model is capable of providing realistic predictions concerning the response of steel fibre reinforced concrete structural configurations exhibiting both ductile and brittle modes of failure without requiring recalibration.

Integrated Proteomics Identified Up-regulated Focal Adhesion-mediated Proteins In Human Squamous Cell Carcinoma In An Orthotopic Murine Model.

Understanding the molecular mechanisms of oral carcinogenesis will yield important advances in diagnostics, prognostics, effective treatment, and outcome of oral cancer. Hence, in this study we have investigated the proteomic and peptidomic profiles by combining an orthotopic murine model of oral squamous cell carcinoma (OSCC), mass spectrometry-based proteomics and biological network analysis. Our results indicated the up-regulation of proteins involved in actin cytoskeleton organization and cell-cell junction assembly events and their expression was validated in human OSCC tissues. In addition, the functional relevance of talin-1 in OSCC adhesion, migration and invasion was demonstrated. Taken together, this study identified specific processes deregulated in oral cancer and provided novel refined OSCC-targeting molecules.

Electronic And Structural Study Of Pt-modified Au Vicinal Surfaces: A Model System For Pt-au Catalysts.

Two single crystalline surfaces of Au vicinal to the (111) plane were modified with Pt and studied using scanning tunneling microscopy (STM) and X-ray photoemission spectroscopy (XPS) in ultra-high vacuum environment. The vicinal surfaces studied are Au(332) and Au(887) and different Pt coverage (θPt) were deposited on each surface. From STM images we determine that Pt deposits on both surfaces as nanoislands with heights ranging from 1 ML to 3 ML depending on θPt. On both surfaces the early growth of Pt ad-islands occurs at the lower part of the step edge, with Pt ad-atoms being incorporated into the steps in some cases. XPS results indicate that partial alloying of Pt occurs at the interface at room temperature and at all coverage, as suggested by the negative chemical shift of Pt 4f core line, indicating an upward shift of the d-band center of the alloyed Pt. Also, the existence of a segregated Pt phase especially at higher coverage is detected by XPS. Sample annealing indicates that the temperature rise promotes a further incorporation of Pt atoms into the Au substrate as supported by STM and XPS results. Additionally, the catalytic activity of different PtAu systems reported in the literature for some electrochemical reactions is discussed considering our findings.