Correlation-type structure activity relationships for the kinetics of gas-phase RO2 self-reactions and reaction with HO2

Structure activity relationships (SARs) are presented for the gas-phase reactions of RO2 with HO2, and the self- and cross-reactions of RO2. For RO2+HO2 the SAR is based upon a correlation between the logarithm of the measured rate coefficient and a calculated ionisation potential for the molecule R-CH=CH2, R being the same group in both the radical and molecular analogue. The correlation observed is strong and only for one RO2 species does the measured rate coefficient deviate by more than a factor of two from the linear least-squares regression line. For the self- and cross-reactions of RO2 radicals, the SAR is based upon a correlation between the logarithm of the measured rate coefficient and the calculated electrostatic potential (ESP) at the equivalent carbon atom in the RH molecule to which oxygen is attached in RO2, again R being the same group in the molecule and the radical. For cases where R is a simple alkyl-group, a strong linear correlation observed. For RO2 radicals which contain lone pair-bearing substituents and for which the calculated ESP<-0.05 self-reaction rate coefficients appear to be insensitive to the value of the ESP. For RO2 of this type with ESP>-0.05 a linear relationship between log k and the ESP is again observed. Using the relationships, 84 out of the 85 rate coefficients used to develop the SARs are predicted to within a factor of three of their measured values. A relationship is also presented that allows the prediction of the Arrhenius parameters for the self-reactions of simple alkyl RO2 radicals. On the basis of the correlations, predictions of room-temperature rate coefficients are made for a number of atmospherically important peroxyl-peroxyl radical reactions. (C) 2003 Elsevier Ltd. All rights reserved.

The influence of ribosome modulation factor on the survival of stationary-phase Escherichia coli during acid stress

Ribosome modulation factor (RMF) was shown to have an influence on the survival of Escherichia coli under acid stress during stationary phase, since the viability of cultures of a mutant strain lacking functional RMF decreased more rapidly than that of the parent strain at pH 3. Loss of ribosomes was observed in both strains when exposed to low pH, although this occurred at a higher rate in the RMF-deficient mutant strain, which also suffered from higher levels of rRNA degradation. It was concluded that the action of RMF in limiting the damage to rRNA contributed to the protection of E coli under acid stress. Expression of the rmf gene was lower during stationary phase after growth in acidified media compared to media containing no added acid, and the increased rmf expression associated with transition from exponential phase to stationary phase was much reduced in acidified media. It was demonstrated that RMF was not involved in the stationary-phase acid-tolerance response in E coli by which growth under acidic conditions confers protection against subsequent acid shock. This response was sufficient to overcome the increased vulnerability of the RMF-deficient mutant strain to acid stress at pH values between 6.5 and 5.5.

Detection of neural correlates of self-paced motor activity using empirical mode decomposition phase locking analysis

Transient episodes of synchronisation of neuronal activity in particular frequency ranges are thought to underlie cognition. Empirical mode decomposition phase locking (EMDPL) analysis is a method for determining the frequency and timing of phase synchrony that is adaptive to intrinsic oscillations within data, alleviating the need for arbitrary bandpass filter cut-off selection. It is extended here to address the choice of reference electrode and removal of spurious synchrony resulting from volume conduction. Spline Laplacian transformation and independent component analysis (ICA) are performed as pre-processing steps, and preservation of phase synchrony between synthetic signals. combined using a simple forward model, is demonstrated. The method is contrasted with use of bandpass filtering following the same preprocessing steps, and filter cut-offs are shown to influence synchrony detection markedly. Furthermore, an approach to the assessment of multiple EEG trials using the method is introduced, and the assessment of statistical significance of phase locking episodes is extended to render it adaptive to local phase synchrony levels. EMDPL is validated in the analysis of real EEG data, during finger tapping. The time course of event-related (de)synchronisation (ERD/ERS) is shown to differ from that of longer range phase locking episodes, implying different roles for these different types of synchronisation. It is suggested that the increase in phase locking which occurs just prior to movement, coinciding with a reduction in power (or ERD) may result from selection of the neural assembly relevant to the particular movement. (C) 2009 Elsevier B.V. All rights reserved.

Self-assembly of an amyloid peptide fragment–PEG conjugate: lyotropic phase formation and influence of PEG crystallization

The self-assembly of PEGylated peptides containing a modified sequence from the amyloid beta peptide, YYKLVFF, has been studied in aqueous solution. Two PEG molar masses, PEG1k and PEG3k, were used in the conjugates. It is shown that both YYKLVFF–PEG hybrids form fibrils comprising a peptide core and a PEG corona. The fibrils are much longer for YYKLVFF–PEG1k, pointing to an influence of PEG chain length. The beta-sheet secondary structure of the peptide is retained in the conjugate. Lyotropic liquid crystal phases, specifically nematic and hexagonal columnar phases, are formed at sufficiently high concentration. Flow alignment of these mesophases was investigated by small-angle neutron scattering with in situ steady shearing in a Couette cell. On drying, PEG crystallization occurs leading to characteristic peaks in the X-ray diffraction pattern, and to lamellar structures imaged by atomic force microscopy. The X-ray diffraction pattern retains features of the cross-beta pattern from the beta-sheet structure, showing that this is not disrupted by PEG crystallization.

Self-assembly of a modified amyloid peptide fragment: pH-responsiveness and nematic phase formation

The self-assembly of peptide YYKLVFFC based on a fragment of the amyloid beta (A) peptide, A beta 16-20, KLVFF has been studied in aqueous solution. The peptide is designed with multiple functional residues to examine the interplay between aromatic interactions and charge on the self-assembly, as well as specific transformations such as the pH-induced phenol-phenolate transition of the tyrosine residue. Circular dichroism (CD) and Fourier-transform infrared (FTIR) spectroscopies are used to investigate the conditions for beta-sheet self-assembly and the role of aromatic interactions in the CD spectrum as a function of pH and concentration. The formation of well-defined fibrils at pH 4.7 is confirmed by cryo-TEM (transmission electron microscope) and negative stain TEM. The morphology changes at higher pH, and aggregates of short twisted fibrils are observed at pH 11. Polarized optical microscopy shows birefringence at a low concentration (1 wt.-%) of YYKLVFFC in aqueous solution, and small-angle X-ray scattering was used to probe nematic phase formation in more detail. A pH-induced transition from nematic to isotropic phases is observed on increasing pH that appears to be correlated to a reduction in aggregate anisotropy upon increasing pH.

Modulation of visually evoked cortical fMRI responses by phase of ongoing occipital alpha oscillations

Using simultaneous electroencephalography as a measure of ongoing activity and functional magnetic resonance imaging (fMRI) as a measure of the stimulus-driven neural response, we examined whether the amplitude and phase of occipital alpha oscillations at the onset of a brief visual stimulus affects the amplitude of the visually evoked fMRI response. When accounting for intrinsic coupling of alpha amplitude and occipital fMRI signal by modeling and subtracting pseudo-trials, no significant effect of prestimulus alpha amplitude on the evoked fMRI response could be demonstrated. Regarding the effect of alpha phase, we found that stimuli arriving at the peak of the alpha cycle yielded a lower blood oxygenation level-dependent (BOLD) fMRI response in early visual cortex (V1/V2) than stimuli presented at the trough of the cycle. Our results therefore show that phase of occipital alpha oscillations impacts the overall strength of a visually evoked response, as indexed by the BOLD signal. This observation complements existing evidence that alpha oscillations reflect periodic variations in cortical excitability and suggests that the phase of oscillations in postsynaptic potentials can serve as a mechanism of gain control for incoming neural activity. Finally, our findings provide a putative neural basis for observations of alpha phase dependence of visual perceptual performance.

Multidecadal modulation of El Nino-Southern Oscillation (ENSO) variance by Atlantic Ocean sea surface temperatures

Observations suggest a possible link between the Atlantic Multidecadal Oscillation (AMO) and El Nino Southern Oscillation (ENSO) variability, with the warm AMO phase being related to weaker ENSO variability. A coupled ocean-atmosphere model is used to investigate this relationship and to elucidate mechanisms responsible for it. Anomalous sea surface temperatures (SSTs) associated with the positive AMO lead to change in the basic state in the tropical Pacific Ocean. This basic state change is associated with a deepened thermocline and reduced vertical stratification of the equatorial Pacific ocean, which in turn leads to weakened ENSO variability. We suggest a role for an atmospheric bridge that rapidly conveys the influence of the Atlantic Ocean to the tropical Pacific. The results suggest a non-local mechanism for changes in ENSO statistics and imply that anomalous Atlantic ocean SSTs can modulate both mean climate and climate variability over the Pacific.

Top-down solar modulation of climate: evidence for centennial-scale change

During the descent into the recent ‘exceptionally’ low solar minimum, observations have revealed a larger change in solar UV emissions than seen at the same phase of previous solar cycles. This is particularly true at wavelengths responsible for stratospheric ozone production and heating. This implies that ‘top-down’ solar modulation could be a larger factor in long-term tropospheric change than previously believed, many climate models allowing only for the ‘bottom-up’ effect of the less-variable visible and infrared solar emissions. We present evidence for long-term drift in solar UV irradiance, which is not found in its commonly used proxies. In addition, we find that both stratospheric and tropospheric winds and temperatures show stronger regional variations with those solar indices that do show long-term trends. A top-down climate effect that shows long-term drift (and may also be out of phase with the bottom-up solar forcing) would change the spatial response patterns and would mean that climate-chemistry models that have sufficient resolution in the stratosphere would become very important for making accurate regional/seasonal climate predictions. Our results also provide a potential explanation of persistent palaeoclimate results showing solar influence on regional or local climate indicators.

The phenology and potential for self-pollination of two Australian monoecious fig species

In this preliminary study, the reproductive phenology of two monoecious fig species, Ficus racemosa and F. rubiginosa, was examined in tropical Australia. Syconia (inflorescences) occurred on both species all year round, but pre-floral and interfloral syconia were much commoner than the wasp-receptive and wasp-emitting phases in both species. The temporal overlap of the wasp-receptive and wasp-emitting phases on a single tree indicated that self-pollination was possible in both species and that pollinators may sometimes persist through multiple generations on one tree. This sexual phase overlap was commoner in F. rubiginosa than in F racemosa. The two species also differed in their general within-tree asynchrony, with a higher diversity of phases on F. rubiginosa than on F. racemosa. The time from syconium initiation to ripening was very similar in F. rubiginosa (mean = 48.51 days) and F. racemosa (mean = 43.53 days). However, there was much more variation within and between trees for F. rubiginosa. In addition, the wasp-receptive phase was found to last up to 5 days (rnean = 4.38) in F. rubiginosa. Such longevity should contribute substantially to local pollinator population persistence. Future work should use genetic studies to determine whether self-pollination is common in these fig species.

Low-molecular-weight gelators: Elucidating the principles of gelation based on gelator solubility and a cooperative self-assembly model

This paper highlights the key role played by solubility in influencing gelation and demonstrates that many facets of the gelation process depend on this vital parameter. In particular, we relate thermal stability (T-gel) and minimum gelation concentration (MGC) values of small-molecule gelation in terms of the solubility and cooperative self-assembly of gelator building blocks. By employing a van't Hoff analysis of solubility data, determined from simple NMR measurements, we are able to generate T-calc values that reflect the calculated temperature for complete solubilization of the networked gelator. The concentration dependence of T-calc allows the previously difficult to rationalize "plateau-region" thermal stability values to be elucidated in terms of gelator molecular design. This is demonstrated for a family of four gelators with lysine units attached to each end of an aliphatic diamine, with different peripheral groups (Z or Bee) in different locations on the periphery of the molecule. By tuning the peripheral protecting groups of the gelators, the solubility of the system is modified, which in turn controls the saturation point of the system and hence controls the concentration at which network formation takes place. We report that the critical concentration (C-crit) of gelator incorporated into the solid-phase sample-spanning network within the gel is invariant of gelator structural design. However, because some systems have higher solubilities, they are less effective gelators and require the application of higher total concentrations to achieve gelation, hence shedding light on the role of the MGC parameter in gelation. Furthermore, gelator structural design also modulates the level of cooperative self-assembly through solubility effects, as determined by applying a cooperative binding model to NMR data. Finally, the effect of gelator chemical design on the spatial organization of the networked gelator was probed by small-angle neutron and X-ray scattering (SANS/SAXS) on the native gel, and a tentative self-assembly model was proposed.

Self-assembly of two-component gels: stoichiometric control and component selection

Two-component systems capable of self-assembling into soft gel-phase materials are of considerable interest due to their tunability and versatility. This paper investigates two-component gels based on a combination of a L-lysine-based dendron and a rigid diamine spacer (1,4-diaminobenzene or 1,4-diaminocyclohexane). The networked gelator was investigated using thermal measurements, circular dichroism, NMR spectroscopy and small angle neutron scattering (SANS) giving insight into the macroscopic properties, nanostructure and molecular-scale organisation. Surprisingly, all of these techniques confirmed that irrespective of the molar ratio of the components employed, the "solid-like" gel network always consisted of a 1:1 mixture of dendron/diamine. Additionally, the gel network was able to tolerate a significant excess of diamine in the "liquid-like" phase before being disrupted. In the light of this observation, we investigated the ability of the gel network structure to evolve from mixtures of different aromatic diamines present in excess. We found that these two-component gels assembled in a component-selective manner, with the dendron preferentially recognising 1,4-diaminobenzene (>70%). when similar competitor diamines (1,2- and 1,3-diaminobenzene) are present. Furthermore, NMR relaxation measurements demonstrated that the gel based oil 1,4-diaminobenzene was better able to form a selective ternary complex with pyrene than the gel based oil 1,4-diaminocyclohexane, indicative of controlled and selective pi-pi interactions within a three-component assembly. As such, the results ill this paper demonstrate how component selection processes in two-component gel systems call control hierarchical self-assembly.

Formation of fibrillar structures through self-assembly of designed peptide turns

Three tripeptides Boc-Phe-Aib-Val-OMe (1), Boc-Leu-Aib-p-NA-NO2 (2) and Boc-Pro-Aib-m-NA-NO2 (3) (Aib: alpha-aminoisobutyric acid; p- and m-NA: para- and meta-nitroaniline) have been designed by incorporating aromatic rings to study the self-assembly and fibril formation. Single crystal X-ray diffraction studies show that all the peptides adopt turn-like structures that are self-assembled through intermolecular hydrogen bonds and van der Waals interactions to create layers of beta-sheets. Solvent dependent NMR titration and CD studies show that the turn structures of the peptides also exist in the solution phase. The field emission scanning electron microscopic (FE-SEM) images of the peptides in the solid state reveal fibrillar structures of flat morphology that are formed through beta-sheet mediated self-assembly of the preorganized turn building blocks.

Design of supramolecular beta-sheet forming beta-turns containing aromatic rings and non-coded alpha-aminoisobutyric acid and the formation of flat fibrillar structures through self-assembly

Single crystal X-ray diffraction studies show that the three designed tripeptides Boc-Leu-Aib-m-NA-NO2 (I), Boc-Phe-Aib-m-NA-NO2 (II) and Boc-Pro-Aib-m-ABA-OMe (III) (Aib, -aminoisobutyric acid; m-NA, m-nitroaniline; m-ABA, m-aminobenzoic acid; Boc, t-butyloxycarbonyl) containing aromatic rings in the backbones adopt -turn structures that are self-assembled through intermolecular hydrogen bonds and van der Waals interactions to create layers of -sheets. Solvent-dependent NMR titration and CD studies show that the -turn structures of the peptides also exist in the solution phase. The field emission scanning electron microscopic and transmission electron microscopic images of the peptides in the solid state reveal fibrillar structures of flat morphology that are formed through -sheet mediated self-assembly of the preorganised -turn building blocks.

Self-assembly of peptide nanotubes in an organic solvent

The self-assembly of a modified fragment of the amyloid beta peptide, based on sequence A beta(16-20), KLVFF, extended to give AAKLVFF is studied in methanol. Self-assembly into peptide nanotubes is observed, as confirmed by electron microscopy and small-angle X-ray scattering. The secondary structure of the peptide is probed by FTIR and circular dichroism, and UV/visible spectroscopy provides evidence for the important role of aromatic interactions between phenylalanine residues in driving beta-sheet self-assembly. The beta-sheets wrap helically to form the nanotubes, the nanotube wall comprising four wrapped beta-sheets. At higher concentration, the peptide nanotubes form a nematic phase that exhibits spontaneous flow alignment as observed by small-angle neutron scattering.

Quantitative model for the kinetics of lyotropic phase transitions involving changes in monolayer curvature

We present a kinetic model for transformations between different self-assembled lipid structures. The model shows how data on the rates of phase transitions between mesophases of different geometries can be used to provide information on the mechanisms of the transformations and the transition states involved. This can be used, for example, to gain an insight into intermediate structures in cell membrane fission or fusion. In cases where the monolayer curvature changes on going from the initial to the final mesophase, we consider the phase transition to be driven primarily by the change in the relaxed curvature with pressure or temperature, which alters the relative curvature elastic energies of the two mesophase structures. Using this model, we have analyzed previously published kinetic data on the inter-conversion of inverse bicontinuous cubic phases in the 1-monoolein-30 wt% water system. The data are for a transition between QII(G) and QII(D) phases, and our analysis indicates that the transition state more closely resembles the QII(D) than the QII(G) phase. Using estimated values for the monolayer mean curvatures of the QII(G) and QII(D) phases of -0.123 nm(-1) and -0.133 nm(-1), respectively, gives values for the monolayer mean curvature of the transition state of between -0.131 nm(-1) and -0.132 nm(-1). Furthermore, we estimate that several thousand molecules undergo the phase transition cooperatively within one "cooperative unit", equivalent to 1-2 unit cells of QII(G) or 4-10 unit cells of QII(D).