Pressure-dependent 13C chemical shifts in proteins: Origins and applications

Pressure-dependent (13)C chemical shifts have been measured for aliphatic carbons in barnase and Protein G. Up to 200 MPa (2 kbar), most shift changes are linear, demonstrating pressure-independent compressibilities. CH(3), CH(2) and CH carbon shifts change on average by +0.23, -0.09 and -0.18 ppm, respectively, due to a combination of bond shortening and changes in bond angles, the latter matching one explanation for the gamma-gauche effect. In addition, there is a residue-specific component, arising from both local compression and conformational change. To assess the relative magnitudes of these effects, residue-specific shift changes for protein G were converted into structural restraints and used to calculate the change in structure with pressure, using a genetic algorithm to convert shift changes into dihedral angle restraints. The results demonstrate that residual (13)C alpha shifts are dominated by dihedral angle changes and can be used to calculate structural change, whereas (13)C beta shifts retain significant dependence on local compression, making them less useful as structural restraints

A note on brain actuated spelling with the Berlin brain-computer interface

Brain-Computer Interfaces (BCIs) are systems capable of decoding neural activity in real time, thereby allowing a computer application to be directly controlled by the brain. Since the characteristics of such direct brain-tocomputer interaction are limited in several aspects, one major challenge in BCI research is intelligent front-end design. Here we present the mental text entry application ‘Hex-o-Spell’ which incorporates principles of Human-Computer Interaction research into BCI feedback design. The system utilises the high visual display bandwidth to help compensate for the extremely limited control bandwidth which operates with only two mental states, where the timing of the state changes encodes most of the information. The display is visually appealing, and control is robust. The effectiveness and robustness of the interface was demonstrated at the CeBIT 2006 (world’s largest IT fair) where two subjects operated the mental text entry system at a speed of up to 7.6 char/min

Utilization and accumulation of compatible solutes in Halomonas pacifica: a species of moderately halophilic bacteria isolated from a saline lake in South Libya

When grown in high salt concentrations, halophilic bacteria often accumulate compatible solutes, which have major applications in biotechnology because they stabilize cells and proteins. Four Gram-negative bacterial strains, belonging to the family Halomonadaceae, were isolated from Qaberoun and Um-Alma lakes in South Libya using high-salinity medium. The strains were identified using 16S rRNA gene sequencing as belonging to Halomonas pacifica (strain ABQ1), Halomonas venusta (ABQ2), Halomonas elongata (ABU1) and Halomonas salifodinae (ABU2). H. pacifica ABQ1 is a moderate halophile (salinity range 0.05 to 2.5 M NaCl), with a broad tolerance to pH (7 to 9) and temperature (25–37 °C). Addition of the compatible solutes glycine betaine (betaine) and ectoine (1,4,5,6-tetrahydro-2-methyl-4-pyrimidine carboxylic acid) to the medium had a positive effect on growth of H. pacifica at 2 M NaCl. In rich LB medium, betaine was the major compatible solute accumulated, with ectoine only being accumulated at salinities in excess of 1 M NaCl. In minimal M9 medium, betaine was not produced, but increasing amounts of ectoine were synthesized with increasing salinity, and hydroxyectoine [(4S,5S)−5-hydroxy-2-methyl-1,4,5,6-tetrahydropyrimidine-4-carboxylic acid] was also synthesized when the cells were grown in very high salt. We have thus identified H. pacifica as a producer of ectoine and hydroxyectoine, with more being produced at higher salinities. As industrial demand for these compatible solutes continues to increase, this system has biotechnological potential

Estimating available salt volume for potential CAES development: a case study using the Northwich Halite of the Cheshire Basin

The massively bedded rock salts forming the Northwich Halite Member of the Cheshire Basin represent a huge mineral resource, which historically, have been worked by dry mining for rock salt and brine production from both the area of wet rockhead and also from solution-mined caverns. More recently, the halite beds have also provided the host storage horizon for natural gas storage in specifically designed and constructed solution-mined salt caverns. Increasingly, compressed air energy storage (CAES) is being viewed as a viable bulk storage option for surplus electrical energy, which may be through the use of off-peak electricity from both conventional and renewable sources. We describe a novel technique using Esri’s ArcGIS® Geographic Information System software, to derive potential storage cavern locations and an estimate of the physical volumes that might be available for storage purposes, including for CAES. The process involves defining the spatial distribution, thickness and insoluble content of the halite beds is described, together with an estimate of the potential physical volumes of solution-mined caverns. Cavern volumes compare favourably with those of current gas storage facilities, which are illustrated in terms of their surface footprints and use of resource

Darkness visible: reflections on underground ecology

1 Soil science and ecology have developed independently, making it difficult for ecologists to contribute to urgent current debates on the destruction of the global soil resource and its key role in the global carbon cycle. Soils are believed to be exceptionally biodiverse parts of ecosystems, a view confirmed by recent data from the UK Soil Biodiversity Programme at Sourhope, Scotland, where high diversity was a characteristic of small organisms, but not of larger ones. Explaining this difference requires knowledge that we currently lack about the basic biology and biogeography of micro-organisms. 2 It seems inherently plausible that the high levels of biological diversity in soil play some part in determining the ability of soils to undertake ecosystem-level processes, such as carbon and mineral cycling. However, we lack conceptual models to address this issue, and debate about the role of biodiversity in ecosystem processes has centred around the concept of functional redundancy, and has consequently been largely semantic. More precise construction of our experimental questions is needed to advance understanding. 3 These issues are well illustrated by the fungi that form arbuscular mycorrhizas, the Glomeromycota. This ancient symbiosis of plants and fungi is responsible for phosphate uptake in most land plants, and the phylum is generally held to be species-poor and non-specific, with most members readily colonizing any plant species. Molecular techniques have shown both those assumptions to be unsafe, raising questions about what factors have promoted diversification in these fungi. One source of this genetic diversity may be functional diversity. 4 Specificity of the mycorrhizal interaction between plants and fungi would have important ecosystem consequences. One example would be in the control of invasiveness in introduced plant species: surprisingly, naturalized plant species in Britain are disproportionately from mycorrhizal families, suggesting that these fungi may play a role in assisting invasion. 5 What emerges from an attempt to relate biodiversity and ecosystem processes in soil is our extraordinary ignorance about the organisms involved. There are fundamental questions that are now answerable with new techniques and sufficient will, such as how biodiverse are natural soils? Do microbes have biogeography? Are there rare or even endangered microbes

Computer simulations of hard pear-shaped particles

We report results obtained from Monte Carlo simulations investi- gating mesophase formation in two model systems of hard pear-shaped particles. The first model considered is a hard variant of the trun- cated Stone-Expansion model previously shown to form nematic and smectic mesophases when embedded within a 12-6 Gay-Berne-like po- tential [1]. When stripped of its attractive interactions, however, this system is found to lose its liquid crystalline phases. For particles of length to breadth ratio k = 3, glassy behaviour is seen at high pressures, whereas for k = 5 several bi-layer-like domains are seen, with high intradomain order but little interdomain orientational correlation. For the second model, which uses a parametric shape parameter based on the generalised Gay-Berne formalism, results are presented for particles with elongation k = 3; 4 and 5. Here, the systems with k = 3 and 4 fail to display orientationally ordered phases, but that with k = 5 shows isotropic, nematic and, unusually for a hard-particle model, interdigitated smectic A2 phases.</p

Actinobacillus pleuropneumoniae serovar 8 predominates in England and Wales

This work was supported by a Longer and Larger (LoLa) grant from the Biotechnology and Biological Sciences Research Council (BBSRC grant numbers BB/G020744/1, BB/G019177/1, BB/G019274/1 and BB/G018553/1) and Zoetis (formerly Pfizer Animal Health) awarded to the Bacterial Respiratory Diseases of Pigs-1 Technology (BRaDP1T) Consortium

Many-body-QED perturbation theory: Connection to the Bethe-Salpeter equation

The connection between many-body theory (MBPT)--in perturbative and non-perturbative form--and quantum-electrodynamics (QED) is reviewed for systems of two fermions in an external field. The treatment is mainly based upon the recently developed covariant-evolution-operator method for QED calculations [Lindgren et al. Phys. Rep. 389, 161 (2004)], which has a structure quite akin to that of many-body perturbation theory. At the same time this procedure is closely connected to the S-matrix and the Green's-function formalisms and can therefore serve as a bridge between various approaches. It is demonstrated that the MBPT-QED scheme, when carried to all orders, leads to a Schroedinger-like equation, equivalent to the Bethe-Salpeter (BS) equation. A Bloch equation in commutator form that can be used for an "extended" or quasi-degenerate model space is derived. It has the same relation to the BS equation as has the standard Bloch equation to the ordinary Schroedinger equation and can be used to generate a perturbation expansion compatible with the BS equation also for a quasi-degenerate model space.Comment: Submitted to Canadian J of Physic

Comparative study of density functional theories of the exchange-correlation hole and energy in silicon

We present a detailed study of the exchange-correlation hole and exchange-correlation energy per particle in the Si crystal as calculated by the Variational Monte Carlo method and predicted by various density functional models. Nonlocal density averaging methods prove to be successful in correcting severe errors in the local density approximation (LDA) at low densities where the density changes dramatically over the correlation length of the LDA hole, but fail to provide systematic improvements at higher densities where the effects of density inhomogeneity are more subtle. Exchange and correlation considered separately show a sensitivity to the nonlocal semiconductor crystal environment, particularly within the Si bond, which is not predicted by the nonlocal approaches based on density averaging. The exchange hole is well described by a bonding orbital picture, while the correlation hole has a significant component due to the polarization of the nearby bonds, which partially screens out the anisotropy in the exchange hole.Comment: 16 pages, 5 figures, RevTeX, added conten

Measurement of the Transverse-Longitudinal Cross Sections in the p (e,e'p)pi0 Reaction in the Delta Region

Accurate measurements of the p(e,e?p)pi0 reaction were performed at Q^2=0.127(GeV/c)^2 in the Delta resonance energy region. The experiments at the MIT-Bates Linear Accelerator used an 820 MeV polarized electron beam with the out of plane magnetic spectrometer system (OOPS). In this paper we report the first simultaneous determination of both the TL and TL? (``fifth" or polarized) cross sections at low Q^{2} where the pion cloud contribution dominates the quadrupole amplitudes (E2 and C2). The real and imaginary parts of the transverse-longitudinal cross section provide both a sensitive determination of the Coulomb quadrupole amplitude and a test of reaction calculations. Comparisons with model calculations are presented. The empirical MAID calculation gives the best overall agreement with this accurate data. The parameters of this model for the values of the resonant multipoles are |M_{1+}(I=3/2)|= (40.9 \pm 0.3)10^{-3}/m_pi, CMR= C2/M1= -6.5 \pm 0.3%, EMR=E2/M1=-2.2 \pm 0.9%, where the errors are due to the experimental uncertainties.Comment: 10 pages, 3 figures, minor corrections and addition